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Does glnexus only load variants contained in the bed file into the db? or all of the variants?
xshah updated
4 years ago
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Improve VCF2Genome to be able to read a normal VCF file (not EMIT_ALL_SITES, rather EMIT_CONFIDENT_SITES or
EMIT_DEFAULT)
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## Bug Report
### Affected tool(s) or class(es)
HaplotypeCaller
### Affected [Version 4.1.5.0](https://github.com/broadinstitute/gatk/tree/4.1.5.0)
- [GATK 4.1.5.0 ] public release version
…
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### Background
Sequencing providers, using a service account, will upload a range of files into the gs://cpg-#STACK-upload bucket. These files include CRAM files, gVCF files, etc. * These files will…
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For GVCFs, is there a way to merge two or more existing GenomicsDBs? So that we do not need to backup in case the workspace become corrupted.
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I've recently rewritten our pipeline for build 38, but haven't collected into nf/snakemake yet. I only post this here because some pieces may be relevant, e.g. the pitfalls from slivar for not annotat…
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### Description of feature
Hi!
I was trying out the `joint_germline` option, which produces a multi-sample VCF file from haplotypecaller. It would be helpful to have a similar feature for othe…
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Hi Zilu,
the DENDRO is an wonderful tool. It may be very useful to me. But I have a big problem when I am building the pipeline.
problem:
1. in the example script you show me, you call the indels b…
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I do have >60,000 samples to process together. I was wondering about the fastest way to process: a) Provide a bam file list to call SNPs? b) Merge into a single bam file and call SNPs c) generate gVCF…
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=== Start HAHap phasing ===
Parameters: Minimum mapping quality = 0
Parameters: Threshold of low coverage = Median
Parameters: Minimum junction number = 4
Parameters: Likelihood of P1 and P2 = 0.4…