Hi. I trid to use mpileup to identified the SNP/Indels. The commands I used were:

samtools fillmd –bAr sample.sorted.bam ref.fa > sample.sorted.baq.bam

samtools mpileup -ugf ref.fa aln.bam | bcftools view -bvcg - > var.raw.bcf

bcftools view var.raw.bcf | vcfutils.pl varFilter -D 100 > var.flt.vcf

I saw some of the SNPs that Qual value that low than 20 and Indels that low than 50.The problem is that I don't know if I can just trust this output resutls ar I still need to filter the resutls to make it reliable. If I need to filter, what kand of rule I should use? Thanks a lot.

Here are some of the results:

1. 1102 . C T 3.01 . DP=10;AF1=0.4997;AC1=1;DP4=1,7,2,0;MQ=60;FQ=4.77;PV4=0.067,1,1,1 GT:PL:GQ 0/1:30,0,147:28
2. 14689 . A G 18.1 . DP=10;AF1=0.5;AC1=1;DP4=0,6,0,4;MQ=60;FQ=21;PV4=1,1.1e-05,1,1 GT:PL:GQ 0/1:48,0,116:51
3. 9373 . C A 44 . DP=10;AF1=0.5;AC1=1;DP4=0,6,4,0;MQ=60;FQ=47;PV4=0.0048,0.014,1,1 GT:PL:GQ 0/1:74,0,115:77
4. 6427 . T TT 14.6 . INDEL;DP=9;AF1=0.5025;AC1=1;DP4=0,1,0,2;MQ=56;FQ=-14.7;PV4=1,1,0.12,1 GT:PL:GQ 0/1:52,0,20:23
5. 314 . AA A 18.5 . INDEL;DP=9;AF1=0.5;AC1=1;DP4=4,0,4,0;MQ=60;FQ=18.5;PV4=1,0.0011,1,1 GT:PL:GQ 0/1:56,0,56:56
6. 6068 . GATTAG G 214 . INDEL;DP=9;AF1=1;AC1=2;DP4=0,0,2,7;MQ=60;FQ=-61.5 GT:PL:GQ 1/1:255,27,0:51