Comparing variants in vcf files that have been mapped to GRCh37 and GRCh38

Question

[cl10101]

I have a VCF format file, which contains variants found for file mapped to hg38 (reference from GATK hg38 bundle) and I would like to compare this variants with VCF file from 1000 genome project, which is mapped to GRCh37. By comparing this files I mean finding variants shared by both files. Are the coordinates in this files the same or should I somehow convert them?

Answer 1

[Pierre Lindenbaum]

convert the file with picard LiftoverVcf : https://broadinstitute.github.io/picard/command-line-overview.html#LiftoverVcf then compare How to compare 2 VCF files

[cl10101]

Thank you. Unfortunately I can't find liftover chain file for g1k_v37 to hg38. I was trying to use hg19ToHg38.over.chain from http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/ but output file is empty and all records were rejected. I found out that g1k_v37 is GRCh37 with slight differences.

[Pierre Lindenbaum]

hg19=v37 .

you're looking for http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz if needed convert the chromosomes names by removing the chr prefix .

[cl10101]

Thank you for response. I removed char prefix in hg19ToHg38.over.chain file as you suggested and now I have error:

"Exception in thread "main" htsjdk.tribble.TribbleException: Badly formed variant context at location chr1:789016; getEnd() was 789016 but this VariantContext contains an END key with value 724396"

I would be grateful for any suggestion how to solve this problem.

[Pierre Lindenbaum]

show me

"grep -Fw 789016 your.vcf"

[cl10101]

there is no output for 789016

[Min Dai]

try "grep -Fw 724396 your.vcf"

I got the same problem:

Exception in thread "main" htsjdk.tribble.TribbleException: Badly formed variant context at location 13:32707645; getEnd() was 32707645 but this VariantContext contains an END key with value 33281782

and the corresponding record is:

13  33281782    esv3631727  C   <INS:MT>    100 PASS    AC=154;AF=0.0307508;AN=5008;CIEND=-1,0;CIPOS=0,1;CS=NUMT_umich;END=33281782;NS=2504;SVTYPE=INS;IMPRECISE;DP=15932;EAS_AF=0.0129;AMR_AF=0.0058;AFR_AF=0.0908;EUR_AF=0.001;SAS_AF=0.0164;VT=SV    GT  0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0