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Illumina / REViewer

A tool for visualizing alignments of reads in regions containing tandem repeats
GNU General Public License v3.0
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Allelic Depth (QC metrics) in REViewer #37

Open a7420174 opened 2 years ago

a7420174 commented 2 years ago

Hi Egor,

This issue is from Illumina/ExpansionHunter#150.

Thanks, JaeHyun

egor-dolzhenko commented 2 years ago

Thanks for opening a new issue, JaeHyun. Here is a REViewer binary that will output an allele depth metric for each repeat.

This preliminary version of REViewer creates a separate metrics file for each repeat. Next week we will modify REViewer to output a single file with metrics for all repeats. We will also implement the breakpoint coverage metric that you requested.

a7420174 commented 2 years ago

Many thanks for your support!

a7420174 commented 2 years ago

Hi,

Can I ask another question?

I am seeking STRs that lack supporting reads using REViewer. I found that the count of reads reported by ExpansionHunter and shown in REViewer were different in some cases. Is it possible? Or because of the problem of data?

Here is an example.

chr8    47640678        .       T       <STR1>,<STR7>   .       PASS    END=47640696;REF=6;RL=18;RU=TTG;VARID=chr8_47640678_47640696;REPID=chr8_47640678_47640696       GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC     1/2:SPANNING/SPANNING:1/7:1-1/7-7:8/63:8/24:0/0:73.396552

988-2 chr8_47640678_47640696

egor-dolzhenko commented 2 years ago

Hi JaeHyun. Thanks for reporting this issue. There might be an inconsistency in alignment filtering / interpretation between ExpansionHunter and REViewer that causes the discrepancy in counts of low-quality alignments. Would it be permissible for you to share EH output for this repeat? If yes, could you please send it to me by email?

a7420174 commented 2 years ago

Okay, I'll send you JSON, VCF, and sorted BAMlet for this repeat.

Thanks.

egor-dolzhenko commented 2 years ago

Thank you!

a7420174 commented 2 years ago

Hi

I think providing information from the original BAM you request needs more time. Sorry for that.

Anyway, I got the latest version of REViewer you just released. Does REViewer have an option reporting metrics for all repeats?

Thanks, JaeHyun