#CEU Trio for Varify

This is a Snakemake workflow using the GATK Haplotype Caller, gVCF-merging, and SnpEff-CBMi to generate demo data for Varify.

The BAM files are directly from the ubiquitous CEU(Utah) trio.

• ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/pilot2_high_cov_GRCh37_bams/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.high_coverage.20100311.bam
• ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/pilot2_high_cov_GRCh37_bams/data/NA12891/alignment/NA12891.chrom20.ILLUMINA.bwa.CEU.high_coverage.20100517.bam
• ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/pilot2_high_cov_GRCh37_bams/data/NA12892/alignment/NA12892.chrom20.ILLUMINA.bwa.CEU.high_coverage.20100517.bam

This borrows heavily from The Snakemake Workflow Repository.

• ftp://gsapubftp-anonymous@ftp.broadinstitute.org//bundle/2.8/b37/hapmap_3.3.b37.vcf.gz
• ftp://gsapubftp-anonymous@ftp.broadinstitute.org//bundle/2.8/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz
• ftp://gsapubftp-anonymous@ftp.broadinstitute.org//bundle/2.8/b37/1000G_omni2.5.b37.vcf.gz
• ftp://gsapubftp-anonymous@ftp.broadinstitute.org//bundle/2.8/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz

config.json should be altered as needed. In particular, filter: can be set to hard or vqsr

cd /nas/is1/leipzig/CEU_trio_for_varify
mkdir vcfs gvcfs log bams gatk_resources
. bin/activate
snakemake -j 3 all

If there is intermediate output you need, make it a target, otherwise it will be deleted by Snakemake.

The following output will be produced from snakemake all

• all_varify directory with Manifest ready for Varify
• all.snpeff.vcf - SnpEff-CBMi annotated, filtered VCF
• all.phased.vcf & all_mendelian_violations.txt - a pedigree phased VCF and MVs