test14

README.md

@@ -1,15 +1,21 @@
 # Quality control of germline variants calling results using a Chinese Quartet family
 
-> Author： Run Luyao
+> Author： Chen Haonan
 >
-> E-mail：18110700050@fudan.edu.cn
+> E-mail：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_wgs_big_pipeline.git
 >
-> Last Updates: 2022/4/26
+> Last Updates: 2023/7/20
 
 ## Install
 
+```
+open-choppy-env
+choppy install renluyao/quartet_dna_quality_control_big_pipeline
+```
+## Usage
+
 ```
 open-choppy-env
 choppy install renluyao/quartet_dna_quality_control_big_pipeline
@@ -69,37 +75,54 @@ 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.
 
 ```bash
-${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${recaled_bam} --algo Haplotyper ${sample}_hc.vcf
+# Calling variant
+deepvariant/bin/run_deepvariant --model_type=WGS --ref=${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