multiple bam files with call mode

[rtyags]

Hi Caleb,

I tried running call mode with outputs from multiple 10x runs. I assumed this would end up with similar output files as the individual runs with tenx mode.

So, I expected something like :

arc_mgatk.A.txt.gz                      arc_mgatk.C.txt.gz        arc_mgatk.rds         arc_mgatk.variant_stats.tsv.gz
arc_mgatk.cell_heteroplasmic_df.tsv.gz  arc_mgatk.depthTable.txt  arc_mgatk.signac.rds  arc_mgatk.vmr_strand_plot.png
arc_mgatk.coverage.txt.gz               arc_mgatk.G.txt.gz        arc_mgatk.T.txt.gz    chrM_refAllele.txt

but I only see :

arc_mgatk.A.txt.gz         arc_mgatk.C.txt.gz        arc_mgatk.G.txt.gz  arc_mgatk.signac.rds  chrM_refAllele.txt
arc_mgatk.coverage.txt.gz  arc_mgatk.depthTable.txt  arc_mgatk.rds       arc_mgatk.T.txt.gz

Am I right in assuming that call mode should also result in similar output? If so, do you know what might have gone wrong in this case?

Thanks

[caleblareau]

In short, we only produce the extra files from tenx mode, simply because there are assumptions about the variant calling applicable to that mode rather than the more general cases that call handles; So it’s producing the right outputs. If you used call, you probably treated each sample like a pseudobulk, which may not be the desired behavior ?

On May 2, 2022, at 3:57 PM, rtyags @.**@.>> wrote:

Hi Caleb,

I tried running call mode with outputs from multiple 10x runs. I assumed this would end up with similar output files as the individual runs with tenx mode.

So, I expected something like :

arc_mgatk.A.txt.gz arc_mgatk.C.txt.gz arc_mgatk.rds arc_mgatk.variant_stats.tsv.gz arc_mgatk.cell_heteroplasmic_df.tsv.gz arc_mgatk.depthTable.txt arc_mgatk.signac.rds arc_mgatk.vmr_strand_plot.png arc_mgatk.coverage.txt.gz arc_mgatk.G.txt.gz arc_mgatk.T.txt.gz chrM_refAllele.txt

but I only see :

arc_mgatk.A.txt.gz arc_mgatk.C.txt.gz arc_mgatk.G.txt.gz arc_mgatk.signac.rds chrM_refAllele.txt arc_mgatk.coverage.txt.gz arc_mgatk.depthTable.txt arc_mgatk.rds arc_mgatk.T.txt.gz

Am I right in assuming that call mode should also result in similar output? If so, do you know what might have gone wrong in this case?

Thanks

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