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bcbio / bcbio.variation.recall

Parallel merging, squaring off and ensemble calling for genomic variants
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Ensembl error on DP4 #19

Closed bioinfo-dirty-jobs closed 6 years ago

bioinfo-dirty-jobs commented 6 years ago

I try to merge 3 variant calling but unfortunately I have this error:

/opt/bcbio.variation.recall/bcbio-variation-recall ensemble -c 1 -n 1 --names somaticsniper,varscan  436.merge.bcbio.vcf.gz ~/database/hg19_primary.fa somaticsniper/436.somaticsniper.vcf varscan/436.varscan.snp.vcf 
2018-Jan-31 20:04:09 +0100 Tardis ERROR [bcbio.variation.recall.main] - 
java.lang.IllegalStateException: Incompatible header types, collision between these two types: FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev"> FORMAT=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
      htsjdk.variant.vcf.VCFUtils.smartMergeHeaders       VCFUtils.java:  94
    bcbio.variation.variantcontext/merge-headers/fn  variantcontext.clj: 161
bcbio.variation.variantcontext/write-vcf-w-template  variantcontext.clj: 187
                         clojure.lang.RestFn.invoke         RestFn.java: 573
bcbio.variation.ensemble.intersect/ensemble-vcfs/fn       intersect.clj:  88
   bcbio.variation.ensemble.intersect/ensemble-vcfs       intersect.clj:  86
           bcbio.variation.ensemble.intersect/-main       intersect.clj: 140
                        clojure.lang.RestFn.applyTo         RestFn.java: 137
                                 clojure.core/apply            core.clj: 630
               bcbio.variation.recall.main/-main/fn            main.clj:  34
                  bcbio.variation.recall.main/-main            main.clj:  33
                        clojure.lang.RestFn.applyTo         RestFn.java: 137
                   bcbio.variation.recall.main.main                    :
chapmanb commented 6 years ago

Sorry about the issue. The error looks like somatic sniper and VarScan have incompatible definitions for DP4 so we can't manage to create a merged VCF from them. Your best bet would be to remove DP4 from one of the files using bcftools (http://www.htslib.org/doc/bcftools.html#annotate):

bcftools annotate -x FORMAT/DP4

then hopefully they'll merge cleanly from there. Hope this helps get your analysis finished.

bioinfo-dirty-jobs commented 6 years ago

@chapmanb thanks so much... Now I have this error

opt/bcbio.variation.recall/bcbio-variation-recall ensemble -c 1 -n 2 --names mutect2,varscan 436.merge.bcbio.vcf.gz ~/database/hg19_primary.fa mutect2/436.mutect2.vcf   somaticsniper/436.somaticsniper_clean.vcf 2018-01-31 22:56:16 Tardis ERROR [bcbio.variation.recall.main] - 
java.lang.Exception: Problem retrieving reference variant for {:chr "chr1", :start 762272, :refa "G", :alta ["A"], :end 762273, :vc-indices (1)}: []
chapmanb commented 6 years ago

Following up on this in #21