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Old 01-30-2017, 06:16 AM   #2
Location: Houston

Join Date: Apr 2009
Posts: 12

Originally Posted by clarissaboschi View Post
I am trying to convert some genome coordinates of SNPs in one vcf file using the CrossMap program (

I am having difficulties with the conversion. My vcf file does not have all chromosomes present in the chain file (for example chromosome random, etc), so the conversion is not performed.

Do I need to remove all chromosomes not present in my vcf file from the chain file? (and maybe from the fasta file as well?)

My error message was:
KeyError: "sequence 'chr10_NT_461738v1_random' not present"

This sequence is present only in the chain file, but I am not sure if I should edit the chain file.

Also, Is the chromosome format need to be the same in the 3 files (input, chain and fasta file): Chr1, chr1 or 1?

The error message "sequence 'chr10_NT_461738v1_random' not present" was not issued by CrossMap itself, it could be issued by its dependent package like pysam.

My guess is "chr10_NT_461738v1_random" presents in your VCF file, but absent from your reference FASTA file.
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