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statgen / verifyBamID

http://genome.sph.umich.edu/wiki/VerifyBamID
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--maxdepth #12

Open feihongloveworld opened 5 years ago

feihongloveworld commented 5 years ago

hi sir: i want to use verifybamid on panel data with depth sequencing。 i got Abnormal results when --maxdepth was set as more than 500 and --precise option。 ##########################

sampleid #SNPS #READS AVG_DP Mixed FREEMIX FREELK1 FREELK0 maxdepth

P180905144625-Ge-T-CLN 188 1876 9.98 0 0.01394 714.61 721.41 10 P180905144625-Ge-T-CLN 188 3746 19.93 0 0.00393 1236.12 1240.62 20 P180905144625-Ge-T-CLN 188 5616 29.87 0 0.00425 1776.42 1783.21 30 P180905144625-Ge-T-CLN 188 7486 39.82 0 0.00321 2314.14 2317.53 40 P180905144625-Ge-T-CLN 188 9356 49.77 0 0.00080 2830.36 2831.73 50 P180905144625-Ge-T-CLN 188 11226 59.71 0 0.00059 3348.49 3349.49 60 P180905144625-Ge-T-CLN 188 13096 69.66 0 0.00045 3866.85 3867.58 70 P180905144625-Ge-T-CLN 188 14966 79.61 0 0.00034 4381.09 4381.60 80 P180905144625-Ge-T-CLN 188 16836 89.55 0 0.00028 4904.81 4905.20 90 P180905144625-Ge-T-CLN 188 18706 99.50 0 0.00021 5418.81 5419.06 100 P180905144625-Ge-T-CLN 188 37403 198.95 0 0.00177 10595.54 10621.21 200 P180905144625-Ge-T-CLN 188 55881 297.24 0 0.00121 15717.71 15739.59 300 P180905144625-Ge-T-CLN 188 74214 394.76 0 0.00153 20902.52 20949.03 400 P180905144625-Ge-T-CLN 188 92268 490.79 0 0.07696 26032.38 26175.21 500 P180905144625-Ge-T-CLN 188 109998 585.10 0 0.08725 31089.21 31234.57 600 P180905144625-Ge-T-CLN 188 127167 676.42 0 0.09931 36049.23 36188.41 700 P180905144625-Ge-T-CLN 188 143102 761.18 0 0.09434 40644.07 40834.78 800 P180905144625-Ge-T-CLN 188 158092 840.91 0 0.09997 45060.62 45268.62 900 P180905144625-Ge-T-CLN 188 172014 914.97 0 0.09895 49220.41 49456.08 1000 P180905144625-Ge-T-CLN 188 231049 1228.98 0 0.09853 66838.20 67213.57 2000 P180905144625-Ge-T-CLN 188 232105 1234.60 0 0.09845 67404.91 67780.31 5000 ######### the mix column is contamination level with mix different sample bam； the maxdepth column is --maxdepth option so i could not understand the usefull of option --maxdepth？？？？ need your help very much .................

tfmorris commented 5 years ago

We are seeing similar behavior. Did anyone ever look into this bug report and figure out the root cause?