Region plot: No data for likelihood. Try with lh_lite parameter.

[evayfang2019]

According to the example (region.md), it reported “No data for likelihood. Try with lh_lite parameter”, as shown in the following figure.

.aligned.sort.bam: alignment by minimap2 and sorting by samtools .vcf.gz: snp calling by deepvariant

### Region plot example
# sample1
cnvpytor -root kid.pytor -rd kid.aligned.sort.bam
cnvpytor -root kid.pytor -his 100000
cnvpytor -root kid.pytor -snp kid.minimap2.dpv.vcf.gz
cnvpytor -root kid.pytor -mask_snps
cnvpytor -root kid.pytor -baf 100000

# sample2
cnvpytor -root ma.pytor -rd ma.aligned.sort.bam
cnvpytor -root ma.pytor -his 100000
cnvpytor -root ma.pytor -snp ma.minimap2.dpv.vcf.gz
cnvpytor -root ma.pytor -mask_snps
cnvpytor -root ma.pytor -baf 100000

# sample3
cnvpytor -root pa.pytor -rd pa.aligned.sort.bam
cnvpytor -root pa.pytor -his 100000
cnvpytor -root pa.pytor -snp pa.minimap2.dpv.vcf.gz
cnvpytor -root pa.pytor -mask_snps
cnvpytor -root pa.pytor -baf 100000

# interactive plotting mode with all sample
cnvpytor -root  kid.pytor ma.pytor pa.pytor -view 100000
cnvpytor> set style classic
cnvpytor> set rd_use_mask
cnvpytor> set file_titles kid ma pa
cnvpytor> set panels rd likelihood snp
cnvpytor> set markersize 0.2
cnvpytor> 17:80M-85M
cnvpytor> save image.png
cnvpytor> quit

[arpanda]

For the region plot, precise chromosome names are required. We expect to address this in a future update.

The read depth panel appears to be empty, possibly because of chromosome names. Please verify the presence of the 'chr' prefix in the chromosome names using the ls command. If the 'chr' prefix is present, please attempt it with 'chr17:80M-85M.'

Thank you, Arijit

[evayfang2019]

It works when adding "chr". Thank you!