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KChen-lab / Monopogen

SNV calling from single cell sequencing
GNU General Public License v3.0
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region-file #41

Closed swvanderlaan closed 4 months ago

swvanderlaan commented 5 months ago

I want to process the whole genome. How does Monopogen that the X, Y, XY/PAR1/PAR2, MT chromosome (regions) are noted? I now (naively) have this:

chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr12
chr22
chrX
chrXY
chrY
chrMT
jinzhuangdou commented 4 months ago

Hi, Monopogen does not work on MT/sex chromosomes since we do not prepare for the imputation panel for them. You can set region.lst as (with -t set as 22 for multi-threading function) chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr12 chr22

swvanderlaan commented 4 months ago

Superb. Thanks