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@MattPM > However, you need to also be certain the header which lists the chromosome order / positions also matches the same order above. Would you be able to give...
@MattPM > http://samtools.github.io/bcftools/bcftools.html#reheader This seems to be exactly what I needed, thanks so much!
@XiaofeiSunUCSF It's been a while since running it, so I have to refer to the very _ad hoc_ notes I took. I used reheader as follows; `bcftools reheader -h reheader.txt...
@hyunminkang Upon closer inspection, my 'missing' samples are mostly contained within barcodes determined to be doublets. I'm getting far more doublets than would be expected (about 1/3 of cells). I...
> I have a script to compare the identity of genotypes between VCF and freemuxlet output. Thanks, that would be interesting. I used `bcftools call` to generate the VCF. As...
I ran `bcftools merge` with 4 single-sample VCFs to get this multi-sample VCF; the last 4 columns correspond to the genotype for each of the 4 samples, N1, N2, G1...
That seems to be the case, though I am far from an expert on VCF/variant calling. Presumably `bcftools call` does not report homref genotype in the output. If it's necessary...
@Marwansha I suggest generating _everything_ using the same genome.fa reference genome, namely single-cell and bulk RNA alignment. This prevents conflicting chromosome name/order in downstream analysis.