Comments (2)
brentp
commented on June 3, 2024
No, that's calculated by igv.js on the fly. So it will show in the jigv plot but it's not readily availble to write to text. you can use a pileup tool or a variant caller at specific loci to extract allele depths for given sites.
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asmlgkj
commented on June 3, 2024
yes, pysam can do such work, but not that fast, because mosdepth is so fast, so I wonder if you prepare to add this function into jigv
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Related Issues (20)
- Read sequence is "*" HOT 1
- Windows build HOT 1
- Anotation track HOT 4
- Add bed-format file to sites option?
- Provide small example output HOT 2
- parameter usage for RNA sequencing samples HOT 2
- Custom Template HOT 1
- IDEA: seeing reads for more than one sample without pedigree file HOT 4
- jigv settings for targeted deep sequencing HOT 4
- automatic taking images given list of regions HOT 1
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- Empty output html HOT 1
- vcf sites html does not show alignments HOT 4
- possible to display gene name by default? HOT 3
- customization
- sort by base HOT 3
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- Feature request: find read by name and highlight/color specific read(s) HOT 2
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