Hi,
I was using samtools (0.1.12a) mpileup and found that with the suggested default parameters as
I just got no useful variants:
However, with -B in the parameter as
I got output as follows
Questions:
1. Does this mean that the seq qual (or depth) of my reads is low?
2. Any other parameters for mpileup should be tried?
Many thanks.
I was using samtools (0.1.12a) mpileup and found that with the suggested default parameters as
samtools mpileup -ug -f chrs.fa -r 1:1-100000 s_5_6_aligned.sorted.bam | bcftools view -cv -
I just got no useful variants:
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-sample depth to 8000
##fileformat=VCFv4.0
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s_5_6_aligned.sorted.bam
[afs] 0:0.000 1:0.000 2:0.000
<mpileup> Set max per-sample depth to 8000
##fileformat=VCFv4.0
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s_5_6_aligned.sorted.bam
[afs] 0:0.000 1:0.000 2:0.000
However, with -B in the parameter as
samtools mpileup -Bug -f chrs.fa -r 1:1-100000 s_5_6_aligned.sorted.bam | bcftools view -cv -
I got output as follows
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s_5_6_aligned.sorted.bam
1 10124 . C A 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,1,0;MQ=30 PL 30,3,0
1 10127 . A C 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,1,0;MQ=30 PL 30,3,0
1 10177 . A C 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,1,0;MQ=30 PL 30,3,0
1 10241 . T C 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,1,0;MQ=30 PL 30,3,0
1 17489 . A C 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,0,1;MQ=30 PL 30,3,0
1 20132 . T G 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,1,0;MQ=30 PL 30,3,0
1 69511 . A G 99 . DP=37;AF1=1;CI95=1,1;DP4=0,0,11,26;MQ=26 PL 255,111,0
1 75933 . A C 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,0,1;MQ=30 PL 30,3,0
1 88318 . A C 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,0,1;MQ=30 PL 30,3,0
1 89923 . A C 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,1,0;MQ=30 PL 30,3,0
1 89925 . T G 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,1,0;MQ=30 PL 30,3,0
[afs] 0:17934.984 1:9.871 2:6.145
1 10124 . C A 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,1,0;MQ=30 PL 30,3,0
1 10127 . A C 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,1,0;MQ=30 PL 30,3,0
1 10177 . A C 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,1,0;MQ=30 PL 30,3,0
1 10241 . T C 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,1,0;MQ=30 PL 30,3,0
1 17489 . A C 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,0,1;MQ=30 PL 30,3,0
1 20132 . T G 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,1,0;MQ=30 PL 30,3,0
1 69511 . A G 99 . DP=37;AF1=1;CI95=1,1;DP4=0,0,11,26;MQ=26 PL 255,111,0
1 75933 . A C 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,0,1;MQ=30 PL 30,3,0
1 88318 . A C 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,0,1;MQ=30 PL 30,3,0
1 89923 . A C 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,1,0;MQ=30 PL 30,3,0
1 89925 . T G 3.02 . DP=1;AF1=0.9999;CI95=0.5,1;DP4=0,0,1,0;MQ=30 PL 30,3,0
[afs] 0:17934.984 1:9.871 2:6.145
Questions:
1. Does this mean that the seq qual (or depth) of my reads is low?
2. Any other parameters for mpileup should be tried?
Many thanks.
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