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Ensembl ref and GATK
I have a cancer rna-seq bam file that I would like to use to call variants using MuTect2, but I ran into a couple of errors that I would appreciate some assistance with. Thank you.
The chr notations in my bam file is absent in the reference fasta (Homo_sapiens_assembly19.fasta). I'd rather not change my bam file header using sed and samtools reheader and rather append chr notation into the reference file. Will this mess up the corresponding snp (00-All.vcf)?
Is there a karytypically sorted Ensembl reference (and its corresponding dbSNP vcf) that I can use for GATK workflow?
The biggest issue is "Error: Discordant contig lengths: read MT LN=16571, ref MT LN=16569" when I use picard's reordersam function. This is because the read was aligned against Ensembl reference. Is there a quick fix to resolve this?
EDIT: I should mention that realigning my seq against GATK's reference is not an option because I don't have the original fastq files available.