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brentp / mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
MIT License
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Wrong calculation of minimum coverage? #207

Closed xsoleacha closed 1 year ago

xsoleacha commented 1 year ago

Hi,

I am using mosdepth v0.3.3 and I'm afraid I may not understand the calculation of the minimum coverage reported in the .mosdepth.summary.txt file. I am using a bed file with a single region of interest (1508 bp long), and mosdepth reports that the minimum coverage in this region of interest is 0:

chrom length bases mean min max ID_CAR19_eF1A-WPRE 2442 21487006 8798.94 0 22234 ID_CAR19_eF1A-WPRE_region 1508 21465952 14234.72 0 22234 total 24422 1487006 8798.94 0 22234 total_region 1508 21465952 14234.72 0 22234

However, when I look at the .per-base.bed.gz flie there are no zeros in the region of interest specified in the BED file, from base 369 to 1876 (attached).

As I said, the BED file (zero-based) has a single region of interest and looks like this:

ID_CAR19_eF1A-WPRE 368 1876 CAR19 1 +

Is this an error or am I missing something?

Thanks! LV_11.sorted.per-base.bed.gz

brentp commented 1 year ago

can you share the full command that you ran? and if you can share the first part of the bam/cram file the recreates the issue, that would be very helpful.

xsoleacha commented 1 year ago

Hi Brent, this is the full command. I am computing the coverage for a lentivirus. For simplicity I have shortened the file names:

mosdepth -t 4 -b file.bed -f genome.fa -T 0,1,100,500,1000 LV11 file.cram

What part of the CRAM file do you specifically need?

Thanks!

brentp commented 1 year ago

From your report, it looks like the first 2000 bases of the cram along with the matching section from the reference would be sufficient.

xsoleacha commented 1 year ago

I can send you both the genome and the cram files in private. Should I email you a link with the two files?

brentp commented 1 year ago

Yes bpederse@gmail.com thanks

xsoleacha commented 1 year ago

I just sent you an e-mail with the files.

Thanks a lot!

Xavi.

brentp commented 1 year ago

Thank Xavi, I made a fix and a new release. https://github.com/brentp/mosdepth/releases/tag/v0.3.5

xsoleacha commented 1 year ago

Thanks for the quick fix Brent!

Best regards,

XS.

Xavier Solé Acha, Ph.D. Consultor 1 CORE Biologia Molecular Centre de Diagnòstic Biomèdic (CDB) Hospital Clínic de Barcelona Villarroel 170, Escala 5 Planta 5, 08036 Barcelona Tel: 932 275 400 ext. 1798 @.*** http://cdb.hospitalclinic.org

De: Brent Pedersen @.> Enviat el: divendres, 15 de setembre de 2023 10:24 Per a: brentp/mosdepth @.> A/c: SOLE, XAVIER (CDB) @.>; Author @.> Tema: Re: [brentp/mosdepth] Wrong calculation of minimum coverage? (Issue #207)

Thank Xavi, I made a fix and a new release. https://github.com/brentp/mosdepth/releases/tag/v0.3.5 — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you [ADVERTIMENT] Aquest correu electrònic s’ha originat fora de l'organització. Verifiqui que el remitent i el contingut són segurs sophospsmartbannerend

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