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Hi,
Does these scripts also work when converting copy number findings from VarScan? I see from the other, well-used thread that they work for indels and SNPs at least.
Thanks!
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This subworkflow will cover the gatk4 best practices workflow: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- starting with the analys…
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**Have you checked the [list of proposed rules](https://github.com/Benjamin-Lee/deep-rules/issues?q=is%3Aissue+is%3Aopen+label%3Arule. ) to see if the rule has already been proposed?**
- [X] Yes
…
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Hi Qing,
As you said in Issues #21 , multi-mapping to a combined alignments and strict criterion were used to get the real SNVs and these can be replaced by other methods such as GATK. So should I ru…
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Hi
I have tumor-only WGS, consisting of nodulous and tumorous tissue.
Your program is very interesting because filtering germline mutations in these samples have seemed very difficult and almost imp…
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### Description of the bug
Hi,
I am trying to install this pipeline using conda. The command used is mentioned below. Conda is expecting an environment.yml file to be present inside "raredisease/…
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Hi,
I have aligned the sequence used speedseq align commad,but when I use speedseq var, error is exist quickly.
Commad:speedseq var -o ERS189473 -w -t 12 /share/disk1/xujt/software/SpeedSeq/speedse…
bioxu updated
8 years ago
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I'm not sure if this falls under the umbrella of things miniwdl does, but it would be nice if it could generate a graph file (using DOT or some similar format) from an input WDL. This feature was supp…
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bash-4.2$ /data/CCRBioinfo/dalgleishjl/sv_mapping/svaba/bin/svaba run -t PAMHYN_Tumor.realigned.md.bam -n PAMHYN_Normal.realigned.md.bam -a PAMHYN_discovery_chr22 -k chr22 -G ucsc.hg19.fa -p 2
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I'm running duphold v 0.2.1
The command I am running is:
~/install_crap/duphold/duphold -v ./results.vcf.gz -b /efs/WGS/data/WGS/ILMN_exptA/b37/KC_downsampledBAM_and_VCF/NA24385/40x/S7508/NA2438…