Hi all,
I need clarification on the DPR option (see an example output below). There are
two alleles reported for each locus, however, the DPR field has 3 values at pos
6554 and 4 values at pos 6690. What does the 3rd and 4th value correspond to
(e.g. what nucleotide) in these cases? Thanks!
Cheers,
ChuShin
--
command:
$ samtools mpileup -B -d 10000 -t DP,DPR -uf reference.fa <BAM_FILES>|
bcftools call -cv -o raw.vcf
--
--
output:
seq1 6554 . G A 121.224 .
DP=102;VDB=0.360777;SGB=17.9188;RPB=0.404703;MQB=2.10899e-12;MQSB=0.980733;BQB=0.730302;MQ0F=0.147059;AF1=0.293951;G3=0.669799,2.37878e-06,0.330198;HWE=6.51903e-05;AC1=10;DP4=43,35,21,3;MQ=42;FQ=122.706;PV4=0.0038602,0.458111,9.36477e-23,0.161162
GT:PL:DP:DPR 1/1:61,15,0:5:0,5,0 0/0:0,9,103:3:3,0,0
0/0:0,24,211:8:8,0,0 0/0:0,30,238:10:10,0,0 0/0:0,36,255:12:12,0,0
0/0:0,18,166:6:6,0,0 0/0:0,30,239:10:10,0,0 0/0:0,0,0:0:0,0,0
0/0:0,21,196:7:7,0,0 1/1:99,21,0:7:0,7,0 0/0:0,24,219:8:8,0,0
0/0:0,24,222:8:8,0,0 1/1:18,21,0:7:0,7,0 0/0:0,0,0:0:0,0,0
1/1:28,9,0:3:0,3,0 0/0:0,18,190:6:6,0,0 0/1:22,6,0:2:0,2,0
seq1 6690 . C T 999 .
DP=152;VDB=0.981285;SGB=3.7794;RPB=0.326667;MQB=0;MQSB=8.54057e-07;BQB=1;MQ0F=0.151316;AF1=0.967821;AC1=33;DP4=1,1,86,64;MQ=35;FQ=15.3744;PV4=1,0.39789,0.00644419,0.357468
GT:PL:DP:DPR 1/1:145,39,0:13:0,13,0,0 1/1:157,24,0:8:0,8,0,0
1/1:241,39,0:13:0,13,0,0 1/1:238,33,0:12:0,11,1,0
1/1:255,45,0:15:0,15,0,0 1/1:128,15,0:5:0,5,0,0
1/1:191,30,0:10:0,10,0,0 0/1:0,6,63:2:2,0,0,0 1/1:163,27,0:9:0,9,0,0
1/1:161,30,0:10:0,10,0,0 1/1:255,54,0:18:0,18,0,0
1/1:255,48,0:16:0,16,0,0 1/1:88,24,0:8:0,8,0,0 1/1:51,9,0:3:0,3,0,0
1/1:71,9,0:3:0,3,0,0 1/1:98,9,0:3:0,3,0,0 1/1:39,12,0:4:0,4,0,0
--
------------------------------------------------------------------------------
Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
