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Improve docs for extract_snps.py #19
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Hi @JPFinnigan, This could be happening because your |
Hello, The FASTA file and the snp_file have the same naming convention for chromosomes (chr_). I think this problem may stem from the fact that my snp_file is a .vcf. I was looking through the some other posted issues and it seems as though its not yet possible to pass a .vcf to Either way I wanted to explain myself. I'm sure this has come up in your internal discussions, but we're excited about the potential of using HISAT2 to support alignment against custom reference-graphs created from SNV/INDEL call-sets derived from joint mutation calling from tumor-normal pairs. (e.g a graph reference containing the reference allele, plus germline SNP/INDEL, plus somatic SNP/INDEL). We (cc: @iskandr) would be eager to hear your thoughts. |
Hi @JPFinnigan, There isn't a script to do it from a VCF file, but I think it wouldn't be too hard to write one. I think you'd have to decompose multiallelic variants and normalize them so they are all left shifted first. You can do both of those operations with |
HISAT2 now supports VCF file - see the HISAT2 webpage. I will update the usage information to make clear which files and formats are used. |
Hey Guys,
Quick question re: usage.
What exactly is a [genome_file]? I've tried running this command with FASTA files (e.g. mm10.fa) and the mm10 genes.gtf files successfully used for
$extract_exons.py
and$extract_splice_sites.py
but in both cases I receive the following error:I'm not entirely sure what I'm doing wrong. Any help would be greatly appreciated
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