Raw Brca1/2 Variants In Breast Cancer Patients And Healthy Relatives Produced With Gatk.

Aligned sequencing data is available in the NCBI Sequence Read Archive (SRA, https://www.ncbi.nlm.nih.gov/sra/) under accession SRP095082. Variants were called using GATK HaplotypeCaller (version 3.6). After joint performing joint genotyping multi-sample vcf file was generated. Next, SNPs and indels were extracted into two different vcf files and specific set of filters were applied for each case. <strong>File descriptions</strong> <strong><em>Datasets</em></strong> <strong>BRCA_SNVs.vcf</strong> - this file contains SNPs called with GATK and hard filters applied. Following filtering options were applied: "QD &lt; 2.0", "FS &gt; 60.0", "MQ &lt; 40.0", "MQRankSum &lt; -12.5", "ReadPosRankSum &lt; -8.0", "SB &lt; -0.10" , "DP &lt; 10" , "GQ &lt; 30" , and "SOR &gt; 3.0" <strong>BRCA_indels.vcf</strong> - This file contains indels called with GATK and hard filters applied. Following filtering options were applied: "QD &lt; 2.0", "FS &gt; 200.0", "ReadPosRankSum &lt; -20.0", "InbreedingCoeff &lt; -0.8", "SOR &gt; 10.0". <strong><em>Scripts package (scritps.zip)</em></strong> Scripts.zip file contains scripts and supporting files for genotype calling and filtering. <strong>raw.variant.caling.sh </strong>– bam files preprocessing, alignment refining and raw genotype calling with HaplotypeCaller. <strong>genotyping_and_filtering.sh </strong>– joint genotyping, variant hard filtering and callset refinement. <strong>LIST.txt</strong> – supporting file that contains bam filenames containing aligned reads. <strong>sample_order.txt</strong> – supporting file for sample renaming. <strong><em>Reference files (hg19) used in variant calling scripts</em></strong> Reference files can be downloaded from GATK bundle web-site at https://software.broadinstitute.org/gatk/download/bundle. <strong>ucsc.hg19.fasta</strong> - human genome assembly; <strong>Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz</strong> – set of known indels to be used for local realignment; <strong>1000G_phase1.indels.hg19.sites.vcf.gz</strong> – set of known indels to be used for local realignment; <strong>dbsnp_138.hg19.vcf.gz</strong> – a recent dbSNP release (build 138); <strong>1000G_phase3_v4_20130502.hg19.lifted.sites.vcf</strong> – the latest set from 1000G phase 3 (v4) for genotype refinement.