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Hello Brad,
I tried doing variant calling with gatk and freebayes in the same analysis run using bcbio-nextgen v. 0.7.8. Content of line number `49410` mentioned at the end of the error message is th…
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Hi -
I am testing bcbio at the Texas Advanced Computing Center at UT Austin. We are looking into offering this package to our user community. I did an isolated install without any problems, and now…
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sorry, I cannot find specific code for supporting GATK2.7, can you tell me where it is? i want to add the support of --emitRefConfidence to HaplotypeCaller, please advice.
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I'm a newbie to python and am having trouble understanding why I can't parse my vcf file. Any help would greatly be appreciated!! Thanks so much.
for record in vcf.Reader(open('all.mergedSNPs.vcf',…
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I'm getting this error trying to call variants in a single fq file:
```
[2014-03-11 07:34] rask: Using input YAML configuration: /gpfs/ngs/oncology/Analysis/external/EXT_008_OvationSureSelectCompare/…
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When I try to run FreeBayes with the --only-use-input-alleles option to regenotype indels I am getting a segfault. I have pasted the command and valgrind results below. Running the same command wit…