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Old 04-08-2012, 12:33 AM   #1
AllanLindh
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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.
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Old 04-18-2012, 09:24 PM   #2
AllanLindh
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Location: Santa Cruz, CA, USA, Earth

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Default

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
lue">
##FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of Phred-scaled genotyp
e likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ../KB1il
lumChr9.bam
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.
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