Hi everyone,
As far as we are aware, the alignments available from the UKB have been obtained with BWA MEM against a Hg38. If so, are we right in assuming that alignments to the unplaced contigs (particularly chrUn_GL000220v1) have been preserved?
Cheers,
Fran
Yes, the chrUn_GL000220v1 contig is present in CRAM files available at RAP.
Once you have access to CRAMs you can check which contigs are included using `samtools idxstats`
Best wishes,
Aleks
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That's great to know, thanks.
We are aware we could check for the contig alignments from the CRAM files, but it was important for us to know in advance before we commit to paying upfront (since paying for the computational resources that re-align would entail is completely out of the question at the moment).
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Hello Fan, could you please tell us which dataset you mean?
Hi Ondrej. With UKB I meant UK Biobank. Sorry for not being clearer. I mistakenly assumed this forum was solely for that dataset.
Thanks Fran, and are you referring to WGS or WES? Is it e.g. 200k WGS or 450k WES etc.?
WGS
Hi Fran,
Yes, the chrUn_GL000220v1 contig is present in CRAM files available at RAP.
Once you have access to CRAMs you can check which contigs are included using `samtools idxstats`
Best wishes,
Aleks
That's great to know, thanks.
We are aware we could check for the contig alignments from the CRAM files, but it was important for us to know in advance before we commit to paying upfront (since paying for the computational resources that re-align would entail is completely out of the question at the moment).
Cheers,
Fran
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