chenhaonan
/
quartet_dna_quality_control_wes_big_pipeline
forked from renluyao/quartet_dna_quality_control_wes_big_pipeline
Watch 1
Star 0
Fork 0
Code Issues 0 Pull Requests 0 Releases 1 Wiki Activity
Browse Source

replace sentieon

tags/v0.2.0
Haonan917 1 year ago
parent
1157d777f8
commit
0e6a0ee1ba
10 changed files with 138 additions and 145 deletions
Split View
Diff Options
Show Stats Download Patch File Download Diff File
  1. +33
    -18
      README.md
  2. +3
    -4
      defaults
  3. +13
    -15
      tasks/BQSR.wdl
  4. +8
    -8
      tasks/Dedup.wdl
  5. +6
    -6
      tasks/Haplotyper.wdl
  6. +3
    -4
      tasks/Realigner.wdl
  7. +22
    -11
      tasks/deduped_Metrics.wdl
  8. +7
    -5
      tasks/mapping.wdl
  9. +12
    -16
      tasks/sentieon.wdl
  10. +31
    -58
      workflow.wdl

+ 33
- 18
README.md View File

@@ -1,18 +1,18 @@
# Quality control of germline variants calling results using a Chinese Quartet family

> Author： Run Luyao
> Author： Ren Luyao, Chen Haonan
>
> E-mail：18110700050@fudan.edu.cn
> E-mail：18110700050@fudan.edu.cn, haonanchen0815@163.com
>
> Git: http://47.103.223.233/renluyao/quartet_dna_quality_control_wgs_big_pipeline
> Git: http://choppy.3steps.cn/chenhaonan/quartet_dna_quality_control_wes_big_pipeline.git
>
> Last Updates: 2022/10/31
> Last Updates: 2023/7/31

## Install

```
open-choppy-env
choppy install renluyao/quartet_dna_quality_control_big_pipeline
choppy install chenhaonan/quartet_dna_quality_control_big_pipeline
```

## Introduction
@@ -69,37 +69,56 @@ fastq_screen --aligner <aligner> --conf <config_file> --top <number_of_reads> --

### 2. Genome alignment

####[sentieon-genomics](https://support.sentieon.com/manual/):v2019.11.28
Reads were mapped to the human reference genome GRCh38 using BWA-MEM.SAMTools is a tool used for SAM/BAM file conversion and BAM file sorting.

####[BWA-MEM](https://github.com/lh3/bwa):v0.7.17


Reads were mapped to the human reference genome GRCh38 using Sentieon BWA.

```bash
${SENTIEON_INSTALL_DIR}/bin/bwa mem -M -R "@RG\tID:${group}\tSM:${sample}\tPL:${pl}" -t $nt -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} | ${SENTIEON_INSTALL_DIR}/bin/sentieon util sort -o ${sample}.sorted.bam -t $nt --sam2bam -i -
# Mapping to reference genome, converting sam to bam, sorting bam file
bwa mem -M -R "@RG\tID:${group}\tSM:${sample}\tPL:${pl}" -t $(nproc) -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} | samtools view -bS -@ $(nproc) -
| samtools sort -@ $(nproc) -o ${user_define_name}_${project}_${sample}.sorted.bam -
```

####[SAMTools](https://github.com/samtools/samtools):v1.17

```bash
# Building an index for sorted bam file
samtools index -@ $(nproc) -o ${user_define_name}_${project}_${sample}.sorted.bam.bai ${user_define_name}_${project}_${sample}.sorted.bam
```

### 3. Post-alignment QC

Qualimap and Paicard Tools (implemented by Sentieon) are used to check the quality of BAM files. Deduplicated BAM files are used in this step.
Qualimap and Picard Tools are used to check the quality of BAM files. Deduplicated BAM files are used in this step.

#### [Qualimap](<http://qualimap.bioinfo.cipf.es/>) 2.0.0

```bash
# BAM QC by qualimap
qualimap bamqc -bam <bam_file> -outformat PDF:HTML -nt <threads> -outdir <output_directory> --java-mem-size=32G
```

####[Sentieon-genomics](https://support.sentieon.com/manual/):v2019.11.28
####[Picard](https://github.com/broadinstitute/picard/):v3.0.0

```
${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} --algo CoverageMetrics --omit_base_output ${sample}_deduped_coverage_metrics --algo MeanQualityByCycle ${sample}_deduped_mq_metrics.txt --algo QualDistribution ${sample}_deduped_qd_metrics.txt --algo GCBias --summary ${sample}_deduped_gc_summary.txt ${sample}_deduped_gc_metrics.txt --algo AlignmentStat ${sample}_deduped_aln_metrics.txt --algo InsertSizeMetricAlgo ${sample}_deduped_is_metrics.txt --algo QualityYield ${sample}_deduped_QualityYield.txt --algo WgsMetricsAlgo ${sample}_deduped_WgsMetricsAlgo.txt
```bash
# Remove duplicates
java -jar /usr/local/picard.jar MarkDuplicates -I ${sorted_bam} -O ${sample}.sorted.deduped.bam -M ${sample}_dedup_metrics.txt --REMOVE_DUPLICATES
# Building an index for the sorted and deduplicated bam file
samtools index -@ $(nproc) -o ${sample}.sorted.deduped.bam.bai ${sample}.sorted.deduped.bam
```

### 4. Germline variant calling

HaplotyperCaller implemented by Sentieon is used to identify germline variants.
HaplotyperCaller implemented by Google DeepVariant is used to identify germline variants.

#### [DeepVariant](<https://github.com/google/deepvariant>) 1.5.0

```bash
${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${recaled_bam} --algo Haplotyper ${sample}_hc.vcf
# Calling variant
deepvariant/bin/run_deepvariant --model_type=WES --ref=${ref_dir}/${fasta} --reads=${recaled_bam} --output_vcf=${sample}_hc.vcf --num_shards=$(nproc)
# Building an index for the vcf file
gatk IndexFeatureFile -I ${sample}_hc.vcf -O ${sample}_hc.vcf.idx
```

### 5. Variants Calling QC
@@ -211,11 +230,7 @@ sample_id,project,vcf_D5,vcf_D6,vcf_F7,vcf_M8
| PCT_1X | Fraction of genome with at least 1x coverage |
| PCT_5X | Fraction of genome with at least 5x coverage |
| PCT_10X | Fraction of genome with at least 10x coverage |
| PCT_20X | Fraction of genome with at least 20x coverage |
| PCT_30X | Fraction of genome with at least 30x coverage |
| Fold-80 | Fold-80 penalty |
| On target bases rate | On target bases rate |


####3. variants.calling.qc.txt


+ 3
- 4
defaults View File

@@ -1,6 +1,5 @@
{
"benchmarking_dir": "oss://pgx-result/renluyao/manuscript_v3.0/reference_datasets_v202103/",
"SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
"fasta": "GRCh38.d1.vd1.fa",
"BENCHMARKdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
"dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
@@ -17,8 +16,8 @@
"BIGcluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
"fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",
"FASTQSCREENdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",
"SENTIEON_LICENSE": "192.168.0.55:8990",
"SENTIEONdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2019.11.28",
"REPLACE_SENTIEON_DOCKER": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-replaced:2.0",
"DEEPVARIANT_DOCKER": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/deepvariant:v1.5.0_20230721",
"QUALIMAPdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
"vcf_D5": "",
"benchmark_region": "oss://pgx-result/renluyao/manuscript_v3.0/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed",
@@ -27,4 +26,4 @@
"MENDELIANdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",
"DIYdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:1.5",
"ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"
}
}

+ 13
- 15
tasks/BQSR.wdl View File

@@ -3,7 +3,6 @@ task BQSR {
File ref_dir
File dbsnp_dir
File dbmills_dir
String SENTIEON_INSTALL_DIR
String fasta
String dbsnp
String db_mills
@@ -17,18 +16,21 @@ task BQSR {
command <<<
set -o pipefail
set -e
export SENTIEON_LICENSE=192.168.0.55:8990
nt=$(nproc)
set -e
/usr/local/gatk-4.4.0.0/gatk BaseRecalibrator \
-R ${ref_dir}/${fasta} \
-I ${realigned_bam} \
--known-sites ${dbsnp_dir}/${dbsnp} \
--known-sites ${dbmills_dir}/${db_mills} \
-O ${sample}_recal_data.table

${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${realigned_bam} --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table

${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${realigned_bam} -q ${sample}_recal_data.table --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table.post --algo ReadWriter ${sample}.sorted.deduped.realigned.recaled.bam

${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --algo QualCal --plot --before ${sample}_recal_data.table --after ${sample}_recal_data.table.post ${sample}_recal_data.csv

${SENTIEON_INSTALL_DIR}/bin/sentieon plot QualCal -o ${sample}_bqsrreport.pdf ${sample}_recal_data.csv
/usr/local/gatk-4.4.0.0/gatk ApplyBQSR \
-R ${ref_dir}/${fasta} \
-I ${realigned_bam} \
-bqsr ${sample}_recal_data.table \
-O ${sample}.sorted.deduped.realigned.recaled.bam

/usr/local/samtools-1.17/bin/samtools index -@ $(nproc) -o ${sample}.sorted.deduped.realigned.recaled.bam.bai ${sample}.sorted.deduped.realigned.recaled.bam
>>>
runtime {
docker:docker
@@ -38,11 +40,7 @@ task BQSR {
}

output {
File recal_table = "${sample}_recal_data.table"
File recal_post = "${sample}_recal_data.table.post"
File recaled_bam = "${sample}.sorted.deduped.realigned.recaled.bam"
File recaled_bam_index = "${sample}.sorted.deduped.realigned.recaled.bam.bai"
File recal_csv = "${sample}_recal_data.csv"
File bqsrreport_pdf = "${sample}_bqsrreport.pdf"
}
}

+ 8
- 8
tasks/Dedup.wdl View File

@@ -1,6 +1,4 @@
task Dedup {

String SENTIEON_INSTALL_DIR
File sorted_bam
File sorted_bam_index
String sample = basename(sorted_bam,".sorted.bam")
@@ -12,10 +10,14 @@ task Dedup {
command <<<
set -o pipefail
set -e
export SENTIEON_LICENSE=192.168.0.55:8990
nt=$(nproc)
${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sorted_bam} --algo LocusCollector --fun score_info ${sample}_score.txt
${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sorted_bam} --algo Dedup --rmdup --score_info ${sample}_score.txt --metrics ${sample}_dedup_metrics.txt ${sample}.sorted.deduped.bam

/usr/local/jdk-20.0.1/bin/java -jar /usr/local/picard.jar MarkDuplicates \
-I ${sorted_bam} \
-O ${sample}.sorted.deduped.bam \
-M ${sample}_dedup_metrics.txt \
--REMOVE_DUPLICATES
/usr/local/samtools-1.17/bin/samtools index -@ $(nproc) -o ${sample}.sorted.deduped.bam.bai ${sample}.sorted.deduped.bam
>>>
runtime {
docker:docker
@@ -25,8 +27,6 @@ task Dedup {
}

output {
File score = "${sample}_score.txt"
File dedup_metrics = "${sample}_dedup_metrics.txt"
File Dedup_bam = "${sample}.sorted.deduped.bam"
File Dedup_bam_index = "${sample}.sorted.deduped.bam.bai"
}

+ 6
- 6
tasks/Haplotyper.wdl View File

@@ -1,7 +1,5 @@
task Haplotyper {
File ref_dir
String SENTIEON_INSTALL_DIR
String fasta
File recaled_bam
File recaled_bam_index
@@ -13,9 +11,12 @@ task Haplotyper {
command <<<
set -o pipefail
set -e
export SENTIEON_LICENSE=192.168.0.55:8990
nt=$(nproc)
${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${recaled_bam} --algo Haplotyper ${sample}_hc.vcf
/opt/deepvariant/bin/run_deepvariant \
--model_type=WES \
--ref=${ref_dir}/${fasta} \
--reads=${recaled_bam} \
--output_vcf=${sample}_hc.vcf \
--num_shards=$(nproc)
>>>
runtime {
@@ -27,7 +28,6 @@ command <<<

output {
File vcf = "${sample}_hc.vcf"
File vcf_idx = "${sample}_hc.vcf.idx"
}
}


+ 3
- 4
tasks/Realigner.wdl View File

@@ -3,7 +3,6 @@ task Realigner {
File ref_dir
File dbmills_dir

String SENTIEON_INSTALL_DIR
String fasta

File Dedup_bam
@@ -18,10 +17,10 @@ task Realigner {
command <<<
set -o pipefail
set -e
export SENTIEON_LICENSE=192.168.0.55:8990
nt=$(nproc)
${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} --algo Realigner -k ${dbmills_dir}/${db_mills} ${sample}.sorted.deduped.realigned.bam
/usr/local/jdk-1.8.0/bin/java -jar /usr/local/GenomeAnalysisTK.jar -T RealignerTargetCreator -R ${ref_dir}/${fasta} -nt $nt -I ${Dedup_bam} -known ${dbmills_dir}/${db_mills} -o ${sample}.IndelRealigner.intervals
/usr/local/jdk-1.8.0/bin/java -jar /usr/local/GenomeAnalysisTK.jar -T IndelRealigner -R ${ref_dir}/${fasta} -I ${Dedup_bam} --targetIntervals ${sample}.IndelRealigner.intervals -o ${sample}.sorted.deduped.realigned.bam
/usr/local/samtools-1.17/bin/samtools index -@ $(nproc) -o ${sample}.sorted.deduped.realigned.bam.bai ${sample}.sorted.deduped.realigned.bam
>>>

runtime {

+ 22
- 11
tasks/deduped_Metrics.wdl View File

@@ -2,7 +2,6 @@ task deduped_Metrics {

File ref_dir
File bed
String SENTIEON_INSTALL_DIR
String fasta
File Dedup_bam
File Dedup_bam_index
@@ -18,7 +17,28 @@ task deduped_Metrics {
set -e
export SENTIEON_LICENSE=192.168.0.55:8990
nt=$(nproc)
${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} --interval ${bed} --algo CoverageMetrics --omit_base_output ${sample}_deduped_coverage_metrics --algo MeanQualityByCycle ${sample}_deduped_mq_metrics.txt --algo QualDistribution ${sample}_deduped_qd_metrics.txt --algo GCBias --summary ${sample}_deduped_gc_summary.txt ${sample}_deduped_gc_metrics.txt --algo AlignmentStat ${sample}_deduped_aln_metrics.txt --algo InsertSizeMetricAlgo ${sample}_deduped_is_metrics.txt --algo QualityYield ${sample}_deduped_QualityYield.txt --algo WgsMetricsAlgo ${sample}_deduped_WgsMetricsAlgo.txt --algo HsMetricAlgo --targets_list ${interval_list} --baits_list ${interval_list} ${sample}_deduped_HsMetricAlgo.txt
/usr/local/jdk-20.0.1/bin/java -jar /usr/local/picard.jar CollectAlignmentSummaryMetrics \
-I ${Dedup_bam} \
-O ${sample}_deduped_aln_metrics.txt \
-R ${ref_dir}/${fasta} \
--VALIDATION_STRINGENCY LENIENT
/usr/local/jdk-20.0.1/bin/java -jar /usr/local/picard.jar CollectInsertSizeMetrics \
-I ${Dedup_bam} \
-O ${sample}_deduped_is_metrics.txt \
-H ${sample}_deduped_is_metrics.pdf
/usr/local/jdk-20.0.1/bin/java -jar /usr/local/picard.jar CollectQualityYieldMetrics \
-I ${Dedup_bam} \
-O ${sample}_deduped_QualityYield.txt
/usr/local/jdk-20.0.1/bin/java -jar /usr/local/picard.jar CollectWgsMetrics \
-I ${Dedup_bam} \
-O ${sample}_deduped_WgsMetricsAlgo.txt \
-R ${ref_dir}/${fasta} \
--VALIDATION_STRINGENCY LENIENT
/usr/local/jdk-20.0.1/bin/java -jar /usr/local/picard.jar CollectHsMetrics \
-I ${Dedup_bam} \
-O ${sample}_deduped_HsMetricAlgo.txt \
--TARGET_INTERVALS ${interval_list} \
--BAIT_INTERVALS ${interval_list}
>>>

runtime {
@@ -29,15 +49,6 @@ task deduped_Metrics {
}

output {
File deduped_coverage_metrics_sample_summary = "${sample}_deduped_coverage_metrics.sample_summary"
File deduped_coverage_metrics_sample_statistics = "${sample}_deduped_coverage_metrics.sample_statistics"
File deduped_coverage_metrics_sample_interval_statistics = "${sample}_deduped_coverage_metrics.sample_interval_statistics"
File deduped_coverage_metrics_sample_cumulative_coverage_proportions = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_proportions"
File deduped_coverage_metrics_sample_cumulative_coverage_counts = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_counts"
File deduped_mean_quality = "${sample}_deduped_mq_metrics.txt"
File deduped_qd_metrics = "${sample}_deduped_qd_metrics.txt"
File deduped_gc_summary = "${sample}_deduped_gc_summary.txt"
File deduped_gc_metrics = "${sample}_deduped_gc_metrics.txt"
File dedeuped_aln_metrics = "${sample}_deduped_aln_metrics.txt"
File deduped_is_metrics = "${sample}_deduped_is_metrics.txt"
File deduped_QualityYield = "${sample}_deduped_QualityYield.txt"

+ 7
- 5
tasks/mapping.wdl View File

@@ -5,8 +5,6 @@ task mapping {
File fastq_1
File fastq_2

String SENTIEON_INSTALL_DIR
String SENTIEON_LICENSE
String group
String sample
String project
@@ -19,9 +17,13 @@ task mapping {
command <<<
set -o pipefail
set -e
export SENTIEON_LICENSE=${SENTIEON_LICENSE}
nt=$(nproc)
${SENTIEON_INSTALL_DIR}/bin/bwa mem -M -R "@RG\tID:${group}\tSM:${sample}\tPL:${pl}" -t $nt -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} | ${SENTIEON_INSTALL_DIR}/bin/sentieon util sort -o ${user_define_name}_${project}_${sample}.sorted.bam -t $nt --sam2bam -i -
bwa mem -M -R "@RG\tID:${group}\tSM:${sample}\tPL:${pl}" -t $(nproc) -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} \
| samtools view -bS -@ $(nproc) - \
| samtools sort -@ $(nproc) -o ${user_define_name}_${project}_${sample}.sorted.bam -
samtools index -@ $(nproc) \
-o ${user_define_name}_${project}_${sample}.sorted.bam.bai \
${user_define_name}_${project}_${sample}.sorted.bam
>>>

runtime {

+ 12
- 16
tasks/sentieon.wdl View File

@@ -11,23 +11,19 @@ task sentieon {
String disk_size

command <<<
set -o pipefail
set -o pipefail
set -e

cat ${quality_yield} | sed -n '2,2p' > quality_yield.header
cat ${quality_yield} | sed -n '3,3p' > ${sample}.quality_yield

cat ${wgs_metrics_algo} | sed -n '2,2p' > wgs_metrics_algo.header
cat ${wgs_metrics_algo} | sed -n '3,3p' > ${sample}.wgs_metrics_algo

cat ${aln_metrics} | sed -n '2,2p' > aln_metrics.header
cat ${aln_metrics} | sed -n '5,5p' > ${sample}.aln_metrics

cat ${is_metrics} | sed -n '2,2p' > is_metrics.header
cat ${is_metrics} | sed -n '3,3p' > ${sample}.is_metrics

cat ${hs_metrics} | sed -n '2,2p' > hs_metrics.header
cat ${hs_metrics} | sed -n '3,3p' > ${sample}.hs_mtrics
cat ${quality_yield} | sed -n '7,7p' > quality_yield.header
cat ${quality_yield} | sed -n '8,8p' > ${sample}.quality_yield
cat ${wgs_metrics_algo} | sed -n '7,7p' > wgs_metrics_algo.header
cat ${wgs_metrics_algo} | sed -n '8,8p' > ${sample}.wgs_metrics_algo
cat ${aln_metrics} | sed -n '7,7p' > aln_metrics.header
cat ${aln_metrics} | sed -n '10,10p' > ${sample}.aln_metrics
cat ${is_metrics} | sed -n '7,7p' > is_metrics.header
cat ${is_metrics} | sed -n '8,8p' > ${sample}.is_metrics

cat ${hs_metrics} | sed -n '7,7p' > hs_metrics.header
cat ${hs_metrics} | sed -n '8,8p' > ${sample}.hs_mtrics


>>>

+ 31
- 58
workflow.wdl View File

@@ -43,9 +43,9 @@ workflow {{ project_name }} {

File bed

String SENTIEON_INSTALL_DIR
String SENTIEON_LICENSE
String SENTIEONdocker
String REPLACE_SENTIEON_DOCKER
String DEEPVARIANT_DOCKER
String FASTQCdocker
String FASTQSCREENdocker
String QUALIMAPdocker
@@ -92,8 +92,6 @@ workflow {{ project_name }} {

call mapping.mapping as mapping_D5 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
SENTIEON_LICENSE=SENTIEON_LICENSE,
pl=pl,
fasta=fasta,
ref_dir=ref_dir,
@@ -102,7 +100,7 @@ workflow {{ project_name }} {
group=project,
sample='LCL5',
project=project,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}
@@ -133,10 +131,9 @@ workflow {{ project_name }} {

call Dedup.Dedup as Dedup_D5 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
sorted_bam=mapping_D5.sorted_bam,
sorted_bam_index=mapping_D5.sorted_bam_index,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}
@@ -153,13 +150,12 @@ workflow {{ project_name }} {

call deduped_Metrics.deduped_Metrics as deduped_Metrics_D5 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
fasta=fasta,
ref_dir=ref_dir,
bed=bed,
Dedup_bam=Dedup_D5.Dedup_bam,
Dedup_bam_index=Dedup_D5.Dedup_bam_index,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
interval_list=bed_to_interval_list.interval_list,
disk_size=disk_size,
cluster_config=BIGcluster_config
@@ -177,44 +173,42 @@ workflow {{ project_name }} {
disk_size=disk_size
}

## Bam realignment doesn't support in GATK 4
call Realigner.Realigner as Realigner_D5 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
fasta=fasta,
ref_dir=ref_dir,
Dedup_bam=Dedup_D5.Dedup_bam,
Dedup_bam_index=Dedup_D5.Dedup_bam_index,
db_mills=db_mills,
dbmills_dir=dbmills_dir,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}

call BQSR.BQSR as BQSR_D5 {
call BQSR.BQSR as BQSR_D5{
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
fasta=fasta,
ref_dir=ref_dir,
realigned_bam=Realigner_D5.realigner_bam,
realigned_bam_index=Realigner_D5.realigner_bam_index,
realigned_bam=Realigner_M8.realigner_bam,
realigned_bam_index=Realigner_M8.realigner_bam_index,
db_mills=db_mills,
dbmills_dir=dbmills_dir,
dbsnp=dbsnp,
dbsnp_dir=dbsnp_dir,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}

call Haplotyper.Haplotyper as Haplotyper_D5 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
fasta=fasta,
ref_dir=ref_dir,
recaled_bam=BQSR_D5.recaled_bam,
recaled_bam_index=BQSR_D5.recaled_bam_index,
docker=SENTIEONdocker,
docker=DEEPVARIANT_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}
@@ -244,8 +238,6 @@ workflow {{ project_name }} {

call mapping.mapping as mapping_D6 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
SENTIEON_LICENSE=SENTIEON_LICENSE,
pl=pl,
fasta=fasta,
ref_dir=ref_dir,
@@ -254,7 +246,7 @@ workflow {{ project_name }} {
group=project,
sample='LCL6',
project=project,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}
@@ -285,10 +277,9 @@ workflow {{ project_name }} {

call Dedup.Dedup as Dedup_D6 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
sorted_bam=mapping_D6.sorted_bam,
sorted_bam_index=mapping_D6.sorted_bam_index,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}
@@ -305,14 +296,13 @@ workflow {{ project_name }} {

call deduped_Metrics.deduped_Metrics as deduped_Metrics_D6 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
fasta=fasta,
ref_dir=ref_dir,
bed=bed,
Dedup_bam=Dedup_D6.Dedup_bam,
Dedup_bam_index=Dedup_D6.Dedup_bam_index,
interval_list=bed_to_interval_list.interval_list,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}
@@ -331,21 +321,19 @@ workflow {{ project_name }} {

call Realigner.Realigner as Realigner_D6 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
fasta=fasta,
ref_dir=ref_dir,
Dedup_bam=Dedup_D6.Dedup_bam,
Dedup_bam_index=Dedup_D6.Dedup_bam_index,
db_mills=db_mills,
dbmills_dir=dbmills_dir,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}

call BQSR.BQSR as BQSR_D6 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
fasta=fasta,
ref_dir=ref_dir,
realigned_bam=Realigner_D6.realigner_bam,
@@ -354,19 +342,18 @@ workflow {{ project_name }} {
dbmills_dir=dbmills_dir,
dbsnp=dbsnp,
dbsnp_dir=dbsnp_dir,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}

call Haplotyper.Haplotyper as Haplotyper_D6 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
fasta=fasta,
ref_dir=ref_dir,
recaled_bam=BQSR_D6.recaled_bam,
recaled_bam_index=BQSR_D6.recaled_bam_index,
docker=SENTIEONdocker,
docker=DEEPVARIANT_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}
@@ -396,8 +383,6 @@ workflow {{ project_name }} {
call mapping.mapping as mapping_F7 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
SENTIEON_LICENSE=SENTIEON_LICENSE,
pl=pl,
fasta=fasta,
ref_dir=ref_dir,
@@ -406,7 +391,7 @@ workflow {{ project_name }} {
group=project,
sample='LCL7',
project=project,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}
@@ -437,10 +422,9 @@ workflow {{ project_name }} {

call Dedup.Dedup as Dedup_F7 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
sorted_bam=mapping_F7.sorted_bam,
sorted_bam_index=mapping_F7.sorted_bam_index,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}
@@ -457,14 +441,13 @@ workflow {{ project_name }} {

call deduped_Metrics.deduped_Metrics as deduped_Metrics_F7 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
fasta=fasta,
ref_dir=ref_dir,
bed=bed,
Dedup_bam=Dedup_F7.Dedup_bam,
Dedup_bam_index=Dedup_F7.Dedup_bam_index,
interval_list=bed_to_interval_list.interval_list,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}
@@ -483,21 +466,19 @@ workflow {{ project_name }} {

call Realigner.Realigner as Realigner_F7 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
fasta=fasta,
ref_dir=ref_dir,
Dedup_bam=Dedup_F7.Dedup_bam,
Dedup_bam_index=Dedup_F7.Dedup_bam_index,
db_mills=db_mills,
dbmills_dir=dbmills_dir,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}

call BQSR.BQSR as BQSR_F7 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
fasta=fasta,
ref_dir=ref_dir,
realigned_bam=Realigner_F7.realigner_bam,
@@ -506,19 +487,18 @@ workflow {{ project_name }} {
dbmills_dir=dbmills_dir,
dbsnp=dbsnp,
dbsnp_dir=dbsnp_dir,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}

call Haplotyper.Haplotyper as Haplotyper_F7 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
fasta=fasta,
ref_dir=ref_dir,
recaled_bam=BQSR_F7.recaled_bam,
recaled_bam_index=BQSR_F7.recaled_bam_index,
docker=SENTIEONdocker,
docker=DEEPVARIANT_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}
@@ -548,8 +528,6 @@ workflow {{ project_name }} {
call mapping.mapping as mapping_M8 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
SENTIEON_LICENSE=SENTIEON_LICENSE,
pl=pl,
fasta=fasta,
ref_dir=ref_dir,
@@ -558,7 +536,7 @@ workflow {{ project_name }} {
group=project,
project=project,
sample='LCL8',
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}
@@ -589,10 +567,9 @@ workflow {{ project_name }} {

call Dedup.Dedup as Dedup_M8 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
sorted_bam=mapping_M8.sorted_bam,
sorted_bam_index=mapping_M8.sorted_bam_index,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}
@@ -609,14 +586,13 @@ workflow {{ project_name }} {

call deduped_Metrics.deduped_Metrics as deduped_Metrics_M8 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
fasta=fasta,
ref_dir=ref_dir,
bed=bed,
Dedup_bam=Dedup_M8.Dedup_bam,
Dedup_bam_index=Dedup_M8.Dedup_bam_index,
interval_list=bed_to_interval_list.interval_list,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}
@@ -635,21 +611,19 @@ workflow {{ project_name }} {

call Realigner.Realigner as Realigner_M8 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
fasta=fasta,
ref_dir=ref_dir,
Dedup_bam=Dedup_M8.Dedup_bam,
Dedup_bam_index=Dedup_M8.Dedup_bam_index,
db_mills=db_mills,
dbmills_dir=dbmills_dir,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}

call BQSR.BQSR as BQSR_M8 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
fasta=fasta,
ref_dir=ref_dir,
realigned_bam=Realigner_M8.realigner_bam,
@@ -658,19 +632,18 @@ workflow {{ project_name }} {
dbmills_dir=dbmills_dir,
dbsnp=dbsnp,
dbsnp_dir=dbsnp_dir,
docker=SENTIEONdocker,
docker=REPLACE_SENTIEON_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}

call Haplotyper.Haplotyper as Haplotyper_M8 {
input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
fasta=fasta,
ref_dir=ref_dir,
recaled_bam=BQSR_M8.recaled_bam,
recaled_bam_index=BQSR_M8.recaled_bam_index,
docker=SENTIEONdocker,
docker=DEEPVARIANT_DOCKER,
disk_size=disk_size,
cluster_config=BIGcluster_config
}

Write Preview
Loading…
Cancel
Save