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Dear @chapmanb;
I tried to run tumor-normal paired tutorial as I was able to run bcbionextgen.py without you it would not happen so thanks again). Now I am trying to discover vm because I am really e…
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I need some suggestion on using freebayes. I have a patients DNA whole exome seq data pre and post treatment. I don’t have their matched normal. The goal is to find if the treatment has cause a chang…
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`
wget https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py
python bcbio_nextgen_install.py ~/install/bc --tooldir=~/install/bc-data --genomes hg38 --aligners bwa
`
T…
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I am wondering if is possible to keep only the indel call from GATK caller. I have realized that otherwise I get a large number of SNPs gremline events.
variantcaller: [gatk,gatk-haplotype,varscan,…
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Will be borrowing the methodology from Arjun's pipeline:
https://github.com/arkal/docker_scripts/blob/master/precision_immuno.py
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Like MuTect and VarScan, this is yet another method which is used for analysis of paired normal/tumor samples.
Support needs to be written from scratch.
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todo:
write function that checks varscan output.
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Hello,
I added the following tools to my Dockerfile:
```
RUN install-repository \
"--url https://toolshed.g2.bx.psu.edu -o pjbriggs --name macs21 --panel-section-name NGS:_Peak_Calling_Youtube" \
"--…
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Hi!
Using bam files as input with the `bam_clean: picard` setting in the config file produces an error when bcbio_nextgen is run (see below). Maybe I'm doing something wrong here, or is this a bug?
…
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Hi!
I'm having issues with mutect; a traceback below. I wonder if it might have something to do with mutect running under the systems java (v. 1.8) instead of java version 1.7 that is included with …