help with CrossMap

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3.0 years ago

raalsuwaidi ▴ 100

Hello all,

I would really appreciate your help as I am new to working with different file builds and having a setback lifting a vcf file from build hg38 to hg19. in essence, using CrossMap the chromosome value gets altered. Like for example, below is the code:

CrossMap.py  vcf  hg38ToHg19.over.chain.gz    inpute_hg38.vcf.gz       hg19.fa.gz            output.hg19.vcf

The output file has the value

chr1_gl000192_random    526406  chr1:149144526:SG   G   A   .

While the file have the value

chr1    149144526   chr1:149144526:SG   G   A

The change happens in the CHROM value after using CrossMap. This change stops me from being able to combine all different vcf files for furthiur analysis. Any idea why this is happening or how to stop it?

VCF hg38 hg19 CrossMap • 1.2k views

ADD COMMENT • link 2.8 years ago by raalsuwaidi ▴ 100

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Does this appear for all positions of the chromosome, or just a few? It might be that these particular positions don't have a corresponding position in the target reference and are placed in some "placeholder" contig to be discarded. But I might be wrong, I didn't use CrossMap yet, I'm just planning to do liftover soon and I'm trying to read up on it.