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Chromosome position in VCF file

I am working on wgs dataset and after running bwa, samtools, picard, gatk pipeline and filtering snp, indels got vcf file for further analysis. Now when I check the chromosome position it shows 

#CHROM POS
NC_0121212.5(Accession number)

instead of certain position like chr1.

I will be grateful if someone give the direction to fix the position.

vcf wgs population genetics plink
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written by tothepoint tothepoint

Can you post the first few records from your VCF file?

Also, please use the code format button (the one with 1's and 0's) to format code/file contents. I have edited your question this time, please try to remember to use it in subsequent posts.

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written by jared.andrews07 jared.andrews07

I apologise for the formatting issue. These are the first few line from the vcf file

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 20 NC_010443.5 469 . C CTT 485.64 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.397;DP=77;ExcessHet=3.0103;FS=1.356;MLEAC=1;MLEAF=0.500;MQ=56.43;MQRankSum=-0.69 8;QD=9.34;ReadPosRankSum=0.783;SOR=0.363 GT:AD:DP:GQ:PL 0/1:31,21:52:99:493,0,846 NC_010443.5 469 . C CTT 435.64 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.264;DP=98;ExcessHet=3.0103;FS=4.741;MLEAC=1;MLEAF=0.500;MQ=53.09;MQRankSum=-0.73 5;QD=8.54;ReadPosRankSum=1.510;SOR=0.932 GT:AD:DP:GQ:PL 0/1:32,19:51:99:443,0,911 NC_010443.5 469 . CT C 85.60 my_indel_filter AC=1;AF=0.500;AN=2;BaseQRankSum=1.291;DP=113;ExcessHet=3.0103;FS=1.147;MLEAC=1;MLEAF=0.500;MQ=55.81;MQRankS um=0.947;QD=0.94;ReadPosRankSum=-1.288;SOR=0.453 GT:AD:DP:GQ:PL 0/1:77,14:91:93:93,0,1529.

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written by tothepoint tothepoint

2 answers

Hi, Here are some of the similar posts you can refer to

Replacing the Chr names and position notions in vcf

VCF files: Change Chromosome Notation

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written by Strand NGS • Strand NGS

I got the solution via :VCF files: Change Chromosome Notation

Thanks for the help

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written by tothepoint tothepoint

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