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nspies / svviz2

for visual evaluation of read support for structural variation
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Name of bam file missing to separate reads in pdf #43

Closed jzook closed 7 years ago

jzook commented 7 years ago

You used to have the name of the bam files to know which reads came from each bam file in the pdf, and these now seem to be missing. I've attached a couple examples, and here is the command I ran, though you might want to just grep these 2 IDs from the vcf since otherwise it'll run 100 sites:

genosv --also-plot-context 4000 --outdir /scratch/PI/msalit/jzook/AJTrio/svvizconfirm/union_170509/genosv20a1PBv030bPASSbionanodiffgt300 --ref /scratch/PI/msalit/jzook/references/human_g1k_v37.fasta -V /scratch/PI/msalit/jzook/AJTrio/svvizconfirm/union_170509/union_170509_refalt.2.2.2.clustered.simpleINFO.techcounts.bionanodiffgt300.vcf.gz /scratch/PI/msalit/jzook/AJTrio/PBNGMLR/HG002_PB_70x.bam,sequencer=pacbio /scratch/PI/msalit/jzook/AJTrio/PBNGMLR/HG003_PB_30x.bam,sequencer=pacbio /scratch/PI/msalit/jzook/AJTrio/PBNGMLR/HG004_PB_30x.bam,sequencer=pacbio

HG2_PB_SVrefinePBcRDovetail_7719.del_X_91678133.pdf

HG2_PB_SVrefinePBcRDovetail_7571.SequenceDefinedVariant.22_50933765-50933765.pdf

nspies commented 7 years ago

This should be fixed with nspies/genomeview@d46a9f295e47464a08b2037d8bd9f80cad342067 -- make sure to update your genomeview with pip install -U genomeview