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3 results for “GATK”
Raw BRCA1/2 variants in breast cancer patients and healthy relatives produced with GATK.
<p>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.</p> <p> </p> <p><strong>File descriptions</strong></p> <p><strong><em>Datasets</em></strong></p> <p><strong>BRCA_SNVs.vcf</strong> - this file contains SNPs called with GATK and hard filters applied. Following filtering options were applied: "QD < 2.0", "FS > 60.0", "MQ < 40.0", "MQRankSum < -12.5", "ReadPosRankSum < -8.0", "SB < -0.10" , "DP < 10" , "GQ < 30" , and "SOR > 3.0"</p> <p><strong>BRCA_indels.vcf</strong> - This file contains indels called with GATK and hard filters applied. Following filtering options were applied: "QD < 2.0", "FS > 200.0", "ReadPosRankSum < -20.0", "InbreedingCoeff < -0.8", "SOR > 10.0".</p> <p> </p> <p><strong><em>Scripts package (scritps.zip)</em></strong></p> <p>Scripts.zip file contains scripts and supporting files for genotype calling and filtering. </p> <p><strong>raw.variant.caling.sh </strong>– bam files preprocessing, alignment refining and raw genotype calling with HaplotypeCaller.</p> <p><strong>genotyping_and_filtering.sh </strong>– joint genotyping, variant hard filtering and callset refinement.</p> <p><strong>LIST.txt</strong> – supporting file that contains bam filenames containing aligned reads.</p> <p><strong>sample_order.txt</strong> – supporting file for sample renaming.</p> <p> </p> <p><strong><em>Reference files (hg19) used in variant calling scripts</em></strong></p> <p>Reference files can be downloaded from GATK bundle web-site at https://software.broadinstitute.org/gatk/download/bundle. </p> <p><strong>ucsc.hg19.fasta</strong> - human genome assembly;</p> <p><strong>Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz</strong> – set of known indels to be used for local realignment;</p> <p><strong>1000G_phase1.indels.hg19.sites.vcf.gz</strong> – set of known indels to be used for local realignment;</p> <p><strong>dbsnp_138.hg19.vcf.gz</strong> – a recent dbSNP release (build 138); </p> <p><strong>1000G_phase3_v4_20130502.hg19.lifted.sites.vcf</strong> – the latest set from 1000G phase 3 (v4) for genotype refinement.</p> <p> </p>
VCF, pileup, and other files for Betula analyses using ebg & GATK
<p>These are the VCF, pileup, and input files files produced by the Genome Analysis ToolKit, SAMtools, and our own scripts, respectively, used for comparing the genotypes estimated by the GATK UnifiedGenotyper and the new model for allopolyploids that we introduced in our paper. Additional processing of the files was conducting using Python and R for filtering and extracting error values and read counts (scripts available on GitHub: https://github.com/pblischak/polyploid-genotyping).</p> <p><strong>Main files:</strong></p> <ul> <li>pendula-ug-filtered30.vcf: VCF file from GATK with all called variants for <em>Betula</em> <em>pendula</em> (diploid).</li> <li>filtered30-pendula.pileup: SAMtools pileup file for variant sites identified by GATK in <em>B</em>. <em>pendula</em>.</li> <li>pubescens-ug-filtered30.vcf: VCF file from GATK with all called variants for <em>Betula</em> <em>pubescens</em> (allotetraploid).</li> <li>filtered30-pubescens.pileup: SAMtools pileup file for variant sites identified by GATK in <em>B</em>. <em>pubescens</em>.</li> </ul> <p><strong>Processed files:</strong></p> <ul> <li>filtered30-variants.txt: tab delimited file of shared variants between B. pendula and B. pubescens.</li> <li>filtered30-vcf1.vcf: VCF file for B. pendula with variants extracted from filtered30-variants.txt.</li> <li>filtered30-vcf2.vcf: VCF file for B. pubescens with variants extracted from filtered30-variants.txt.</li> </ul> <p><strong>Input files</strong>:</p> <ul> <li>filtered30-pubescens-tot.txt, filtered30-pubescents-alt.txt, filtered30-pubescens-err.txt: input files for running the alloSNP model in ebg.</li> <li>filtered30-pubescens-alloSNP-freqs2.txt, filtered30-pubescens-alloSNP-g1.txt, filtered30-pubescens-alloSNP-g2.txt: output files from the alloSNP model.</li> <li>filtered30-pendula-tot.txt, filtered30-pendula-alt.txt, filtered30-pendula-err.txt: input files for running the hwe model in ebg.</li> <li>filtered30-pendula-hwe-freqs.txt, filtered30-pendula-hwe-genos.txt: output files from the hwe model. The allele frequency estimates here were also used as the reference panel for the alloSNP model.</li> </ul>
JG2.1.0-Based GATK Resource Bundle
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