Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
New consensus from VCF dbrami Bioinformatics 9 09-20-2012 11:35 PM
vcf-tools vcf-stats sample question Rubal7 Bioinformatics 1 04-09-2012 01:42 AM
How to get list of column in vcf file using jessada Bioinformatics 0 01-20-2012 08:22 AM
Problem with vcf file generated Bioinformatics 0 01-05-2012 04:22 AM
VCFtools problem - broken VCF header on 1000genomes data Bioinformatics 1 07-08-2011 05:17 AM

Thread Tools
Old 04-08-2012, 12:33 AM   #1
Junior Member
Location: Santa Cruz, CA, USA, Earth

Join Date: Apr 2012
Posts: 5
Default Problem with vcf-concat

I am trying to concatenate vcf files from individual Chrm using vcf-concat
no matter what I try, i get following error message and no concatenated file

The column names do not agree in [../Chrm2/Chrm2.vcf].
at /home/allan/src/vcftools_0.1.8a/bin/vcf-concat line 32
main::error('The column names do not agree in [../Chrm2/Chrm2.vcf].\x{a}') called at /home/allan/src/vcftools_0.1.8a/bin/vcf-concat line 114
main::concat('HASH(0x21cf518)') called at /home/allan/src/vcftools_0.1.8a/bin/vcf-concat line 12

Yet as near as I can tell, the two .vcf files have exactly the same columns, nice illumina data, looks clean, something just not right. Thanks

Warning, I am new at this, is probably trivial error. but I've tried for couple days, read everything I can find, searched SeqAnswers, all to no avail.
AllanLindh is offline   Reply With Quote
Old 04-18-2012, 09:24 PM   #2
Junior Member
Location: Santa Cruz, CA, USA, Earth

Join Date: Apr 2012
Posts: 5

The problem is with a mismatch between the vcf format output by samtools/bcftools view, and the input file expected by vcf-concat. Example:
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-va
##FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of Phred-scaled genotyp
e likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
chr9 53 . A . 31.5 . DP=1;AF1=0;AC1=0;DP4=1,0

The "##FORMAT=<ID=PL,Number=-1" is not accepted by vcf-concat, it wants "." instead of a "-1"

In addition, the .bam file name from which the vcf file was constructed ("../KB1illumChr9.bam") must be the same for the two .vcf files being concatinated, which makes no sense if they are from different chromosomes. Only solution I found was to use awk to change the "-1" to a ".", and the specific file name in the header line to a generic name that was the same for all the files being concatinated.
AllanLindh is offline   Reply With Quote

concatenate, vcf, vcf-concat, vcftools

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 07:21 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO