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There aren't enough variants in the 1000g.phase3.100k set for VerifyBamID to work properly for quite a few of the exome samples I've been running. I've generated my own panel using common variants in …
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### Description of the bug
Then GATK4_BEDTOINTERVALLIST sometimes fails when using a variety of references genomes due to the incorrect creation of the genome.dict or exome.bed file from the refere…
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Hi,
I am using `caveman.pl` with Whole Exome sequencing (WXS) data however the execution ends in an error in the `mstep` process (please see the error below), this error occurs for various regions …
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Dear Developer,
I am wondering if there is anyway to use msisensor2 to detect MSI in the whole-exome sequencing data with mouse tumor samples? Do you know if there is any other program that can do …
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Hello Igor,
I am currently extracting STR from 1000 Genome WGS and a WES dataset.
When comparing the distributions of the STRs used in the catalog between the two datasets, I can see some discrep…
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Hi,
I would like to use your tool to create wes reads with CNVs but it fails with segmentation fault on $ref/SInC/SInC_simulate. After debugging a little bit, it looks like the reference file cre…
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Hi there!
I am asking a small issue regarding normalization step, `tri.counts.method` - I am normalizing to hg38 exome but not sure if this can be replaced by the hg19 metrics as the package defaul…
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@dianacornejo see in the screenshot here:
https://github.com/cumc/bioworkflows/issues/132#issuecomment-1014771731
these indels are from the SAME data-set but has two lines of representations. …
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**Describe the bug**
For X-chromosomal variants the number of hemizygous individuals is not displayed in the variant details.
**To Reproduce**
Steps to reproduce the behavior:
1. Filter for X-ch…
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Hello,
I have data where the tumor samples have been sequenced for whole genome whereas the normal samples are whole exome. Can I run these samples as such with facets or should I extract exonic re…