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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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Template command for qsignature #1423

Closed sluke123 closed 8 years ago

sluke123 commented 8 years ago

Template command on the yaml file with qsignature duplicates the entry in the alignment section and the top level of the sample yaml

lpantano commented 8 years ago

Hi,

sorry about that. I am not sure I understand, can you give an example? That way I can try to find the bug and a solution.

cheers

mjafin commented 8 years ago

Instead of this:

- algorithm:
    aligner: false
    mark_duplicates: false
    mixup_check: qsignature
    realign: false
    recalibrate: false
    variantcaller: false
  analysis: variant2
  description: 020-20
  files:
  - /path/to/ready.bam
  genome_build: hg38
  metadata:
    batch: 020-20-batch
    phenotype: tumor

it had 

- algorithm:
    aligner: false
    mark_duplicates: false
    mixup_check: qsignature
    realign: false
    recalibrate: false
    variantcaller: false
  analysis: variant2
  description: 020-20
  files:
  - /path/to/ready.bam
  genome_build: hg38
  mixup_check: qsignature_full
  metadata:
    batch: 020-20-batch
    phenotype: tumor
lpantano commented 8 years ago

I guess your template was?, I am trying to reproduce this and see what is the problem:

- algorithm:
    aligner: false
    mark_duplicates: false
    mixup_check: qsignature
    realign: false
    recalibrate: false
    variantcaller: false
  analysis: variant2
  genome_build: hg38

thanks

sluke123 commented 8 years ago

Actually I had the variantcaller as a list – perhaps it was that giving me a problem? If so please close the issue.

The sample yaml file then had mixup_check: qsignature in the algorithm section, and at the top level.

Sally Luke Associate Principal Scientist

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I guess your template was?, I am trying to reproduce this and see what is the problem:

thanks

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mjafin commented 8 years ago

Here's the template, it was run on bam files:

# Template for paired (tumor/normal) variant calling
# see http://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html for more options!
---
details:
  - analysis: variant2
    genome_build: hg38 # [hg19, GRCh37, mm10, rn5]
    mixup_check: qsignature_full
    # In order to do paired variant calling, samples should belong to the
    # same batch ("batch" under "metadata" below") and have a "phenotype"
    # field stating either "normal" or tumor". For each batch there
    # should be a sample with "tumor" phenotype and a sample with "normal"
    # phenotype (no more than two samples per batch)
    algorithm:
      aligner: false # [bwa, bowtie, bowtie2, mosaik, novoalign, false], set to false for targeted panels that use pcr
      mark_duplicates: false
      recalibrate: false  # [gatk, false]
      realign: false  # [gatk, gkno, false]
      mixup_check: qsignature
      variantcaller: [false] # Valid values are "mutect", "varscan", "freebayes", "vardict"

Edit. Ugh. We put mixup_check there twice in the template ourselves! Oops..

lpantano commented 8 years ago

Hi,

nice, mystery solved!