Haynes Heaton

The alt.mtx and ref.mtx files out of vartrix give the allele counts for each variant for each locus. The format is % comment % comment total_loci total_cells total_entries locus_index cell_index...

Yes, I'm sorry if I misspoke. souporcell_merged_sorted_vcf.vcf is the vcf that gets sent to vartrix so that is the vcf which the matrix files refer to.

I just tested it and it worked for me. In my experience wget from google drive can be wonky and I have sometimes gotten 404 errors. Sometimes retrying immediately has...

But at the same time, I have deleted old versions, so if you post the command you are using, I can check if it is currently still in my google...

It's 3Gb so can't upload it to github. There are other services that might be better options than google drive.

It works for me, but if wget isn't working a directly link is more google drive friendly. Problem with that is that you can't easily download it directly to a...

What is the size of the singularity image (ls -lah souporcell.sif) Also what version of singularity do you have? singularity --version Best, Haynes

can you show me the line in the vcf starting with #CHROM. so just grep '#CHROM' vcf_filename

In the format field you have two colons back yo back. There needs to be a dot between them to indicate no value. Not sure which package im using that...

Oh wait, nvm. That is in the id field