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 .................
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 .................