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variant-calling
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update workflow

master
YaqingLiu 3 years ago
parent
f4279ccb13
commit
3accc366b6
4 changed files with 35 additions and 35 deletions
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  1. +14
    -14
      tasks/processSomatic.wdl
  2. +3
    -3
      tasks/somatic.wdl
  3. +12
    -12
      tasks/somaticFilter.wdl
  4. +6
    -6
      workflow.wdl

+ 14
- 14
tasks/processSomatic.wdl View File

command <<< command <<<
cp ${varscan_snp} ./ cp ${varscan_snp} ./
cp ${varscan_indel} ./ cp ${varscan_indel} ./
java -Xmx16g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.SNP.vcf
java -Xmx16g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.INDEL.vcf
java -Xmx16g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.SNP.vcf
java -Xmx16g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.INDEL.vcf


>>> >>>


} }


output { output {
File varscan_snp_somatic = "${sample}.VarScan.TN.SNP.Somatic.vcf"
File varscan_snp_germline = "${sample}.VarScan.TN.SNP.Germline.vcf"
File varscan_snp_loh = "${sample}.VarScan.TN.SNP.LOH.vcf"
File varscan_snp_somatic_hc = "${sample}.VarScan.TN.SNP.Somatic.hc.vcf"
File varscan_snp_germline_hc = "${sample}.VarScan.TN.SNP.Germline.hc.vcf"
File varscan_snp_loh_hc = "${sample}.VarScan.TN.SNP.LOH.hc.vcf"
File varscan_indel_somatic = "${sample}.VarScan.TN.INDEL.Somatic.vcf"
File varscan_indel_germline = "${sample}.VarScan.TN.INDEL.Germline.vcf"
File varscan_indel_loh = "${sample}.VarScan.TN.INDEL.LOH.vcf"
File varscan_indel_somatic_hc = "${sample}.VarScan.TN.INDEL.Somatic.hc.vcf"
File varscan_indel_germline_hc = "${sample}.VarScan.TN.INDEL.Germline.hc.vcf"
File varscan_indel_loh_hc = "${sample}.VarScan.TN.INDEL.LOH.hc.vcf"
File varscan_snp_somatic = "${sample}.VarScan.SNP.Somatic.vcf"
File varscan_snp_germline = "${sample}.VarScan.SNP.Germline.vcf"
File varscan_snp_loh = "${sample}.VarScan.SNP.LOH.vcf"
File varscan_snp_somatic_hc = "${sample}.VarScan.SNP.Somatic.hc.vcf"
File varscan_snp_germline_hc = "${sample}.VarScan.SNP.Germline.hc.vcf"
File varscan_snp_loh_hc = "${sample}.VarScan.SNP.LOH.hc.vcf"
File varscan_indel_somatic = "${sample}.VarScan.INDEL.Somatic.vcf"
File varscan_indel_germline = "${sample}.VarScan.INDEL.Germline.vcf"
File varscan_indel_loh = "${sample}.VarScan.INDEL.LOH.vcf"
File varscan_indel_somatic_hc = "${sample}.VarScan.INDEL.Somatic.hc.vcf"
File varscan_indel_germline_hc = "${sample}.VarScan.INDEL.Germline.hc.vcf"
File varscan_indel_loh_hc = "${sample}.VarScan.INDEL.LOH.hc.vcf"
} }
} }

+ 3
- 3
tasks/somatic.wdl View File

String disk_size String disk_size


command <<< command <<<
samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somatic --mpileup 1 --min-coverage 3 --min-coverage-normal 3 --min-coverage-tumor 3 --min-var-freq 0.08 --p-value 0.10 --somatic-p-value 0.05 --output-vcf 1 --output-snp ${sample}.VarScan.TN.SNP --output-indel ${sample}.VarScan.TN.INDEL --strand-filter 1
samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somatic --mpileup 1 --min-coverage 3 --min-coverage-normal 3 --min-coverage-tumor 3 --min-var-freq 0.08 --p-value 0.10 --somatic-p-value 0.05 --output-vcf 1 --output-snp ${sample}.VarScan.SNP --output-indel ${sample}.VarScan.INDEL --strand-filter 1
>>> >>>


runtime { runtime {
} }
output { output {
File varscan_snp = "${sample}.VarScan.TN.SNP.vcf"
File varscan_indel = "${sample}.VarScan.TN.INDEL.vcf"
File varscan_snp = "${sample}.VarScan.SNP.vcf"
File varscan_indel = "${sample}.VarScan.INDEL.vcf"
} }
} }

+ 12
- 12
tasks/somaticFilter.wdl View File

String disk_size String disk_size


command <<< command <<<
java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.Somatic.filter.vcf
java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.SNP.Somatic.filter.vcf


java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.Germline.filter.vcf
java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.SNP.Germline.filter.vcf


java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.LOH.filter.vcf
java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.SNP.LOH.filter.vcf


java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.Somatic.filter.vcf
java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.Somatic.filter.vcf


java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.Germline.filter.vcf
java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.Germline.filter.vcf


java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.LOH.filter.vcf
java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.LOH.filter.vcf


# Merge SNP and INDEL # Merge SNP and INDEL
awk '{if ($1!~/^#/) print}' ${sample}.VarScan.TN.SNP.Somatic.filter.vcf | cat ${sample}.VarScan.TN.INDEL.Somatic.filter.vcf - > ${sample}.VarScan.TN.Somatic.filter.vcf
awk '{if ($1!~/^#/) print}' ${sample}.VarScan.TN.SNP.Germline.filter.vcf | cat ${sample}.VarScan.TN.INDEL.Germline.filter.vcf - > ${sample}.VarScan.TN.Germline.filter.vcf
awk '{if ($1!~/^#/) print}' ${sample}.VarScan.TN.SNP.LOH.filter.vcf | cat ${sample}.VarScan.TN.INDEL.LOH.filter.vcf - > ${sample}.VarScan.TN.LOH.filter.vcf
awk '{if ($1!~/^#/) print}' ${sample}.VarScan.SNP.Somatic.filter.vcf | cat ${sample}.VarScan.INDEL.Somatic.filter.vcf - > ${sample}.VarScan.Somatic.filter.vcf
awk '{if ($1!~/^#/) print}' ${sample}.VarScan.SNP.Germline.filter.vcf | cat ${sample}.VarScan.INDEL.Germline.filter.vcf - > ${sample}.VarScan.Germline.filter.vcf
awk '{if ($1!~/^#/) print}' ${sample}.VarScan.SNP.LOH.filter.vcf | cat ${sample}.VarScan.INDEL.LOH.filter.vcf - > ${sample}.VarScan.LOH.filter.vcf
>>> >>>


runtime { runtime {
} }


output { output {
File varscan_somatic_filter = "${sample}.VarScan.TN.Somatic.filter.vcf"
File varscan_germline_filter = "${sample}.VarScan.TN.Germline.filter.vcf"
File varscan_loh_filter = "${sample}.VarScan.TN.LOH.filter.vcf"
File varscan_somatic_filter = "${sample}.VarScan.Somatic.filter.vcf"
File varscan_germline_filter = "${sample}.VarScan.Germline.filter.vcf"
File varscan_loh_filter = "${sample}.VarScan.LOH.filter.vcf"
} }
} }

+ 6
- 6
workflow.wdl View File

input: input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR, SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
SENTIEON_LICENSE=SENTIEON_LICENSE, SENTIEON_LICENSE=SENTIEON_LICENSE,
sample=sample_id + '.N',
sample=sample_id,
fasta=fasta, fasta=fasta,
ref_dir=ref_dir, ref_dir=ref_dir,
recaled_bam=normal_BQSR.recaled_bam, recaled_bam=normal_BQSR.recaled_bam,
if (pindel) { if (pindel) {
call Pindel.Pindel as Pindel { call Pindel.Pindel as Pindel {
input: input:
sample_id=sample_id + '.N',
sample_id=sample_id,
bam=normal_BQSR.recaled_bam, bam=normal_BQSR.recaled_bam,
bam_index=normal_BQSR.recaled_bam_index, bam_index=normal_BQSR.recaled_bam_index,
fasta=fasta, fasta=fasta,
} }
} }


if (varscan) {
if (varscan && normal_fastq_1 != "") {
call somatic.somatic as somatic { call somatic.somatic as somatic {
input: input:
sample=sample_id, sample=sample_id,
input: input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR, SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
SENTIEON_LICENSE=SENTIEON_LICENSE, SENTIEON_LICENSE=SENTIEON_LICENSE,
sample=sample_id + '.N',
sample=sample_id,
fasta=fasta, fasta=fasta,
ref_dir=ref_dir, ref_dir=ref_dir,
recaled_bam=normal_BQSR_fb.recaled_bam, recaled_bam=normal_BQSR_fb.recaled_bam,


if (pindel) { if (pindel) {
call Pindel.Pindel as Pindel_fb { call Pindel.Pindel as Pindel_fb {
input:
sample_id=sample_id + '.N',
input:
sample_id=sample_id,
bam=normal_BQSR_fb.recaled_bam, bam=normal_BQSR_fb.recaled_bam,
bam_index=normal_BQSR_fb.recaled_bam_index, bam_index=normal_BQSR_fb.recaled_bam_index,
fasta=fasta, fasta=fasta,

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