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- [ ] rename wgs_calling_regions_CAW.list for GRCh37
- [x] QC processes do launch with '--noReports' (should not)
- [ ] add check for misspelled parameteres (i.e. adding '--pom file.vcf' is silently…
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https://github.com/oicr-gsi/bamqc/blob/a3964603efc86334e3345d30c331c9aacab256b2/lib/GSI/bamqc.pm#L311-L315
This code adds a new BED record to the `bed` hash, using the BED chrom value as the key. T…
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Hi!
**Description of bug:**
MultiQC run on several qualimap reports does not produce information on each sample
**MultiQC run details (please complete the following):**
- Command used to ru…
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Change Alfred so that it makes both types of bam QCs
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```
> `tools/bamQC.py -i /home/ns5bc/pepatac_test/test1/aligned_hg38/test1_sort.bam -c 1 -o /home/ns5bc/pepatac_test/test1/QC_hg38/test1_bamQC.tsv` (7490)
Traceback (most recent call last):
…
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```
Traceback (most recent call last):
File "tools/bamQC.py", line 242, in
_LOGGER = logger_via_cli(args)
File "/home/ns5bc/.local/lib/python3.6/site-packages/pararead/logs.py", line …
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Hello!
When I turn on the save-bam option, I got the error in below.
`save-bam: true`
> WARNING:toil.leader:9/H/jobIJzf6M Traceback (most recent call last):
> WARNING:toil.leader:9/H/jo…
hmkim updated
5 years ago
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Hi Felix,
I have a questions concerning my data; I'm sorry if it's a stupid question, I'm new to WGBS data, and trying bismark to do the analysis.
I have WGBS data, PE, sequenced using the stand…
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# Describe the bug
I was running an EAGER 2.0.6 run with both samples and blanks.
One of the blanks had no reads hitting to the reference genome, and at `damageprofiler` the pipeline crashed becau…
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`docker tag -f quay.io/ucsc_cgl/bamqc:1.0--a5b6a69bdf4fcc9ef7959d98e53259e0218c7a52 quay.io/ucsc_cgl/bamqc:latest` at https://github.com/BD2KGenomics/cgl-docker-lib/blob/master/bamQC/Makefile#L10 fail…