vcf compare between 2 vcf files using vcf tools

Comparing to vcf files using vcf-compare: The command below runs, but it is very slow, both are indexed by tabix and both vcf files are ~ 2MB. Thank you :).

vcf-compare getrm_NA12878.vcf.gz NA12878.vcf.gz > compare

Is the file format an issue?

head -10 getrm_NA12878.vcf
##fileformat=VCFv4.1
##fileDate=Thu Mar 28 08:49:37 2013
##source= ConvertVCFGetRM to dump from ARUP_NA12878_exome.vcf
##fileDate=Thu Mar 28 10:02:59 2013
##source= ConvertVCFGetRM to dump from ARUP_NA12878_RainDance_Mito.vcf
##fileDate=Thu Mar 28 10:38:24 2013
##source= ConvertVCFGetRM to dump from /netmnt/traces04/sra-ftp-misc/development/get-rm/March_2013/BCM_MGL/VCF/processing_file/BCM-MGL_NA12878_PFIC.txt
##fileDate=Thu Mar 28 10:36:42 2013
##source= ConvertVCFGetRM to dump from /netmnt/traces04/sra-ftp-misc/development/get-rm/March_2013/BCM_MGL/VCF/processing_file/BCM-MGL_NA12878_GSD.txt

 head -10 NA12878.vcf
##fileformat=VCFv4.1
##fileDate=20160428
##fileUTCtime=2016-04-28T07:47:26
##source="tvc 5.0-13 (e975447) - Torrent Variant Caller"
##parametersName="Generic - Proton P1 or S5/S5XL (540) - Germ Line - Low Stringency"
##parametersDetails="germline_low_stringency_p1_540, TS version: 5.0"
##basecallerVersion="5.0-13/e975447"
##tmapVersion="5.0.13 (e975447) (201510291545)"
##reference=/results/referenceLibrary/tmap-f3/hg19/hg19.fasta
##phasing=none

vcftools

• 9,402 views • link

updated 3.4 years ago by Ram

• written 9.7 years ago by bioguy24

I think vcf-compare has been replaced with a faster version now: http://vcftools.sourceforge.net/perl_module.html - A fast htslib C version of this tool is now available (see bcftools stats).

• 0 views • link

written 9.7 years ago by Tonor

That fixed it and the command does run and output a compare file but it does not look right.

bcftools stats getrm_NA12878.vcf.gz NA12878.vcf.gz > compare
[W::vcf_parse] INFO 'AC' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AN' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'SF' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'GENE' is not defined in the header, assuming Type=String
[W::vcf_parse] FILTER 'TruthSensitivityTranche99.00to99.90' is not defined in the header
[W::vcf_parse] INFO 'DB' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DNA' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'RNA' is not defined in the header, assuming Type=String
[E::bcf_calc_ac] todo: 7 at 1:955597

compare (output)
# This file was produced by bcftools stats (1.3.1+htslib-1.3.1) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats  getrm_NA12878.vcf.gz NA12878.vcf.gz
#
# Definition of sets:
# ID    [2]id   [3]tab-separated file names
ID  0   getrm_NA12878.vcf.gz
ID  1   NA12878.vcf.gz
ID  2   getrm_NA12878.vcf.gz    NA12878.vcf.gz

Thank you :).

• 0 views • link

written 9.7 years ago by bioguy24

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