v-a-s-a / galaxy.consensus Goto Github PK

Right now, I'll be adding a minimally valid header and recoding the output vcf file instead of recomputing.

Correct me if I'm wrong, but I believe that there is a small inconsistency with the output VCF file and the VCFv4.1 specification (http://samtools.github.io/hts-specs/VCFv4.1.pdf) section 1.4.2 on Genotype fields.

At the moment a variant is notated as follows:

#CHROM  POS         ID              REF ALT QUAL    FILTER  INFO    FORMAT  1483JS0009
22      17072483    22:17072483:A:G A   G   .       PASS    X1:X2   CN:GT   C:0/1   

I believe the genotype data and its FORMAT should have the GT field at position 0, like:

#CHROM  POS         ID              REF ALT QUAL    FILTER  INFO    FORMAT  1483JS0009
22      17072483    22:17072483:A:G A   G   .       PASS    X1:X2   GT:CN   0/1:C   

I've been having some trouble with a few tools due to this. A small program on my side fixes the problem, but I figured you would like to know about this.

We have an issue of overwriting the database if we run the consensus caller in parallel on a single machine. Essentially, the sqlite3 database file will be overwritten each time.

When you run comparisons, how do you deal with cases where nearby alleles have been merged (clumped)?

As of now, the tables in the db schema are named based on the file names. Change this so that galaxy can rename the input files as a part of its workflows.

I'm trying the example, but it gives these error:

Traceback (most recent call last):
File "./consensus_tool/consensus_genotyper.py", line 37, in
main()
File "./consensus_tool/consensus_genotyper.py", line 32, in main
for records, genotypes in ensemble.concordant_variants(siteThresh=args.siteThresh, genoThresh=args.genoThresh):
File "/opt/galaxy.consensus/consensus_tool/vcf_ensemble.py", line 101, in concordant_variants
yield records, ensemble.set_concordance()
File "/opt/galaxy.consensus/consensus_tool/variant_ensemble.py", line 39, in set_concordance
calls = [ record.genotype(sample).gt_type for record in self.recordSet ]
AttributeError: 'Reader' object has no attribute 'genotype'