update results of NA12878 using official ICE PON (same git hash for t…
…ysis Document contamination downsampling analysis
Make VQSLOD definition accurate
Fix Foxog NaN output and add read stats for indels
…ctions stats for indels (issue 1024) fixed docs
Merge if both GT are phased
…h_new_allele Update the allele remapping code to handle the new spanning deletion allele.
…allele. Now that Ron updated the GATK so that we use star to represent spanning deletions, we need to catch those cases in the code that remaps alleles. Otherwise, we try to pad the stars and that's just bad. Added test from actual failing data.
Indexing parameters not required if output file has the g.vcf.gz exte…
…el_allele_1000 Added else clause to handle symbolic alleles
…ing_dels Handle cases where a given sample has multiple spanning deletions.
When a sample has multiple spanning deletions and we are asked to assign likelihoods to the spanning deletion allele, we currently choose the first deletion. Valentin pointed out that this isn't desired behavior. I promised Valentin that I would address this issue, so here it is. I do not believe that the correct thing to do is to sum the likelihoods over all spanning deletions (I came up with problematic cases where this breaks down). So instead I'm using a simple heuristic approach: using the hom alt PLs, find the most likely spanning deletion for this position and use its likelihoods. In the 10K-sample VCF from Monkol there were only 2 cases that this problem popped up. In both cases the heuristic approach works well.
Enable contamination correction via downsampling (as for HaplotypeCal…
…ler), added test Add oxoG read count annotation and add as default annotation Add ##SAMPLE VCF header line in accordance with TCGA VCF spec, specifying "File" line in sample header with BAM file name and "SampleName" with BAM sample name (Don't print sample file path if --no_cmdline_in_header is specified to help with test consistency) Turn on active region assembly-based physical phasing for M2 Clean up M2-related annotations so UG doesn't crash if M2 annotations are called
Add spannning deletions allele
…ntigs Changed error message for Contigs Out of Order
…_#1002 User (mnw21cam) patch to fix DoC slowdown in 3.4
created panel of normals queue creation script and instructions
Built VectorLoglessPairHMM lib with icc with gcc 4.4.7
Fix loading of VectorLoglessPairHMM by rolling back to Intel's lib version
increased runtime java memory, changed default PON for NN to be new ICE PON updated FP rates, when using new default PON. SNPs up by ~3%, INDELs down by 40% updated git hash reference updated git hash reference
…k_negative_zeros_973_depends_on_841 removed in-line conditional (hack) that changed the result from 0.0 to -0.0; see issue #841