variant calling through gatk

Question

[ashaneev07]

Hello all,

I have been working with a sample dataset and have developed a workflow that generates a VCF file through GATK. This is typically used for identifying genetic variants in human samples. It would mean a lot to me if anyone could kindly review my commands, as your feedback would help boost my confidence in my approach. Only then can I apply this to the original sample.

Thank you..

bwa mem -t 4 -R "@RG\tID:sample003\tPL:ILLUMINA\tSM:sample003" /hg38/hg38.fa sample_R1.fastp.fastq.gz sample_R2.fastp.fastq.gz  > sample003.paired.sam

OR

bwa mem -t 4 -R "@RG\tID:sample003\tPL:ILLUMINA\tSM:sample003" /hg38/hg38.fa sample_R1.fastp.fastq.gz sample_R2.fastp.fastq.gz | samtools view -Sb - > sample003.paired.bam 

samtools view -Sb sample003.paired.sam > sample003.paired.bam
samtools sort sample003.paired.bam -o sample003.paired_sorted.bam

gatk MarkDuplicatesSpark -I sample003.paired_sorted.bam -O sample003.sorted_dedup_reads.bam 

gatk BaseRecalibrator -I sample003.sorted_dedup_reads.bam -R  /hg38/hg38.fa  --known-sites  /hg38/Homo_sapiens_assembly38.dbsnp138.vcf -O recal_data.table 

gatk ApplyBQSR -I sample003.sorted_dedup_reads.bam -R /hg38/hg38.fa --bqsr-recal-file recal_data.table -O sample003_sorted_dedup_bqsr_reads.bam 

gatk CollectAlignmentSummaryMetrics R=/hg38/hg38.fa I=sample003_sorted_dedup_bqsr_reads.bam O=alignment_metrics.txt

gatk HaplotypeCaller -R /hg38/hg38.fa -I sample003_sorted_dedup_bqsr_reads.bam -O 53_raw_variants.vcf --dbsnp /dbsnp/hg38_All_20180418.vcf

gatk SelectVariants  -R /hg38/hg38.fa   -V 53_raw_variants.vcf   -O snps_only.vcf   --select-type-to-include SNP

gatk VariantFiltration \
  -R /hg38/hg38.fa \
  -V snps_only.vcf \
  -O snp.filtered.unnorm.vcf \
  --filter-expression "MQ0 >= 5 && ((MQ0 / (1.0 * DP)) > 0.1)" --filter-name "HARD_TO_VALIDATE" \
  --filter-expression "DP < 10" --filter-name "LowCoverage" \
  --filter-expression "QUAL < 30.0" --filter-name "VeryLowQual" \
  --filter-expression "QUAL > 30.0 && QUAL < 50.0" --filter-name "LowQual" \
  --filter-expression "QD < 1.5" --filter-name "LowQD"

bcftools norm -c w  -f /hg38/hg38.fa  -m -any  -o variants.filtered.norm.vcf.gz   -Oz snp.filtered.unnorm.vcf

[Pierre Lindenbaum]

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