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I run on RHEL 5.5 and I have this error:
I set again the path now I have the right bcftools..
I have this error now
```
~/jdk1.8.0_121/bin/java -XX:+UseSerialGC -Xms1g -Xmx10g -jar /illumin…
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Hi. I tried to run ensemble mode neusomatic.
Since there was no 'SomaticSeq.Wrapper.sh' on 'https://github.com/bioinform/somaticseq/blob/master/SomaticSeq.Wrapper.sh',
I ran 'somaticseq_parallel.py'…
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Greetings,
I have been trying to use seqmule with exome data acquired with illumina nextera rapid capture kit but i am having a problem while extracting consensus calls with gatk's vcfv4.2 support ev…
ghost updated
6 years ago
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With #356, the VCF file created by `intrahost.py`'s `merge_to_vcf` reports read depth, at a given position, only for samples that contain alternate alleles at that position. If a sample has no alterna…
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Hi, thanks for this great tool!
I am not able to run the somatic mutation calls for multiple libraries. I have two runs for the normal and two runs for the tumor. The seqmule pipeline generates the f…
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`git clone https://github.com/jeremiahsavage/cwl_aws_cp.git`
with cwltool:
```
(cwl) [jeremiah@localhost ~]$ cwltool cwl_aws_cp/aws_s3_get.cwl cwl_aws_cp/aws_s3_get.yml
/home/jeremiah/.virtuale…
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I have centos 5.5 I need to try to merge my vcf and then I would like to use ensembl.
I call my variant using mutect1,mutect2,varscan and vardict.
`
> `/jdk1.8.0_121/bin/java -jar bcbio-variation…
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Hi
I have read your exhaustive introduction and paper and I think it can be useful for my purpose. My interest is to study Ecoli within-host diversity for each sample. Basically, each sample is a fas…
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# Modules to be tested
* gistic2 [needs ncurses API 5 compatibility package on Rocky 8]
* r-siteconfig [needs version check]
* snpeff [wrong version installed; snpeff/5.0e (L) snpeff/5.1e s…
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When running SuperFreq without vcf files, I get:
Calls: superFreq -> superFreq -> analyse
In addition: Warning messages:
1: In system("varscan") : error in running command
2: In performPreliminary…