Mark DePristo 1677a0a458 Simpler FILTER and info field encoding for BeagleOutputToVCF ... -- Previous version created FILTERs for each possible alt allele when that site was set to monomorphic by BEAGLE. So if you had a A/C SNP in the original file and beagle thought it was AC=0, then you'd get a record with BGL_RM_WAS_A in the FILTER field. This obviously would cause problems for indels, as so the tool was blowing up in this case. Now beagle sets the filter field to BGL_SET_TO_MONOMORPHIC and sets the info field annotation OriginalAltAllele to A instead. This works in general with any type of allele. -- Here's an example output line from the previous and current versions: old: 20 64150 rs7274499 C . 3041.68 BGL_RM_WAS_A AN=566;DB;DP=1069;Dels=0.00;HRun=0;HaplotypeScore=238.33;LOD=3.5783;MQ=83.74;MQ0=0;NumGenotypesChanged=1;OQ=1949.35;QD=10.95;SB=-6918.88 new: 20 64062 . G . 100.39 BGL_SET_TO_MONOMORPHIC AN=566;DP=1108;Dels=0.00;HRun=2;HaplotypeScore=221.59;LOD=-0.5051;MQ=85.69;MQ0=0;NumGenotypesChanged=1;OQ=189.66;OriginalAltAllele=A;QD=15.81;SB=-6087.15 -- update MD5s to reflect these changes -- [delivers #50847721]		2013-06-14 15:56:13 -04:00
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gatk/walkers	Simpler FILTER and info field encoding for BeagleOutputToVCF	2013-06-14 15:56:13 -04:00
utils	Merge pull request #273 from broadinstitute/rp_readIsPoorlyModelled	2013-06-13 08:40:24 -07:00