Issue with bcftools csq phasing
Hi all!
I want to perform phasing on a .vcf file (Human mtDNA sample). For this purpose I run bcftools csq.
My command is as follows:
bcftools-1.6/bcftools csq -f Human_mito.fasta -g sequence.gff3 -p s sample_fltd.vcf -o trial.out
My gff file is as follows:
##sequence-region NC_012920.1 1 16569
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606
NC_012920.1 RefSeq region 1 16569 . + . ID=NC_012920.1:1..16569;Dbxref=taxon:9606;Is_circular=true;Name=MT;country=United Kingdom: Great Britain;gbkey=Src;genome=mitochondrion;isolation-source=caucasian;mol_type=genomic DNA;note=this is the rCRS;tissue-type=placenta
NC_012920.1 RefSeq sequence_alteration 10 10 . + . ID=id-NC_012920.1:10..10;Dbxref=dbSNP:879233578;gbkey=variation;replace=T
The error it prints is:
csq.c:715 gff_id_parse] Could not parse the line, "Parent=transcript:" not present: NC_012920.1 RefSeq exon 577 647 . +. ID=exon-TRNF-1;Parent=rna-TRNF;Dbxref=GeneID:4558,HGNC:HGNC:7481,MIM:590070;Note=NAR: 1455;anticodon=(pos:611..613);codons=1;gbkey=tRNA;gene=TRNF;product=tRNA-Phe
Any idea how to solve this error? -Thanks
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rabio •
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shubhra.bhattacharya
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shubhra.bhattacharya
1 answer
I was able to fix this by changing the gff file to one from the ensembl ftp: http://ftp.ensembl.org/pub/
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How are the contigs in your VCF named? You should also bgzip and tab-index your VCF, as this can resolve some header issues.
No I have not done that. I'll give it a try!
Okay. Please report back when you have time.