Chromosome position in VCF file

Question

[tothepoint]

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.

[jared.andrews07]

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.

[tothepoint]

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.

Answer 1

[Strand NGS]

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

Answer 2

[tothepoint]

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

Thanks for the help