Problem with normalization by bcftools
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17 months ago
Negin ▴ 20

I used the command below to normalize my vcf file by spliting multiple alternatives into multiple rows:

bcftools norm -m - <in.vcf> > out.vcf

but some of the variants disappeared after normalization!! Does anyone know why this happened?

bcftools vcf files samtools sequencing genomics • 523 views
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Can you provide a specific example of disappearing variants?

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17 months ago
Negin ▴ 20

Here, the example:

Chromosome 2339162 . C T,A 89906.62 PASS AC=25,1; AF=0.114,4.566e-03;AN=219;BaseQRankSum=-3.610e-01;DP=17877;FS=1.706;MLEAC=25,1;M LEAF=0.114,4.566e-03;MQ=60.00;MQRankSum=0.00;QD=34.36;ReadPosRankSum=0.412;SNPEF F_AMINO_ACID_CHANGE=D87Y;SNPEFF_CODON_CHANGE=Gac/Tac;SNPEFF_EFFECT=NON_SYNONYMOU S_CODING;SNPEFF_EXON_ID=1;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=p rotein_coding;SNPEFF_GENE_NAME=gyrA;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID= AAC75291;SOR=0.651 GT:AD:DP:GQ:PL 0:89,0,0:89:99:0,1800,1800 0:86,0,0 :86:99:0,1800,1800 0:78,0,0:78:99:0,1800,1800 0:98,0,0:98:99:0,1800,18 00 0:105,0,0:105:99:0,1800,1800 0:101,0,0:101:99:0,1800,1800 0:98,0,0 :98:99:0,1800,1800

Btw, I didn't copy the genotype fields for all the samples.

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That's not a complete example: you only stated the input, not the output and what was missing from it. Imagine yourself on the other side of this: what information would you need to reproduce the problem at all? If we can't do that, we can't really help.

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Because I can't post a long reply, I show only the variant that was part of the input, but it disappeared from the output. I hope this is helpful. Otherwise, which kind of information do you need?

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Can you reproduce the problem by pasting just that line into a VCF file, and then copying over a bunch of header lines? If not, we have no hope; we don't even have access to the header lines which you haven't posted, or the bcftools version, or...

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