1,120
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Filtering a VCF file
A example command line of upgrading / filtering a glfMultiples output is as follows.
A example command line of upgrading / filtering a glfMultiples output is as follows.
vcfCooker --in-vcf /home/csidore/1000g_CEUTSI_WG/analysis_chr20/vcf/TSI+CEU+GBR.Q10.chr20.vcf --out 1KG.20100517.EUR.chr20.vcf.gz --bgzf --upgrade --filter --maxAB 65 --indelVCF /share/swg/hmkang/data/1000G/pilot_indels_2010_07/1kg.pilot_release.merged.indels.sites.hg19.chr20.vcf --winIndel 10 --minDP 93 --maxDP 1860 --minNS 19 --minQUAL 10 --write-vcf --winFFRQ 10 --maxFFRQ 30
vcfCooker --in-vcf /home/csidore/1000g_CEUTSI_WG/analysis_chr20/vcf/TSI+CEU+GBR.Q10.chr20.vcf --out 1KG.20100517.EUR.chr20.vcf.gz --bgzf --upgrade \
--filter --maxAB 65 --indelVCF /share/swg/hmkang/data/1000G/pilot_indels_2010_07/1kg.pilot_release.merged.indels.sites.hg19.chr20.vcf --winIndel 10 --minDP 93 --maxDP 1860 --minNS 19 --minQUAL 10 --write-vcf --winFFRQ 10 --maxFFRQ 30
== Acknowledgements ==
== Acknowledgements ==
VerifyBamID is a result from collaborative effort by Hyun Min Kang, Matthew Flickenger, Matthew Snyder, Paul Anderson, Tom Blackwell, Mary Kate Trost, and Goncalo Abecasis. Please email to Hyun Min Kang [[mailto:hmkang@umich.edu| hmkang@umich.edu ]] for any questions.
VerifyBamID is a result from collaborative effort by Hyun Min Kang, Matthew Flickenger, Matthew Snyder, Paul Anderson, Tom Blackwell, Mary Kate Trost, and Goncalo Abecasis. Please email to Hyun Min Kang [[mailto:hmkang@umich.edu| hmkang@umich.edu ]] for any questions.
