Question

I Did A Samtools Pileup And Ended In A Vcf Format Like This

0

Entering edit mode

12.1 years ago

satish.nair • 0

Hi Everyone

I was doing the samtools mpileup piping with bcftools using this command ("samtools mpileup -uf hg19.fa SingleCell5.chrM.bam | bcftools view -cg -v - > test3") and ended up in a vcf format like this. I actually want to see the variants in this chromosome and got a doubt at the two bold lines that I have shown below . What does that really mean? An INDEL is there? If then what the INDEL is exactly because in the Alt section it is showing a dot which makes me confuse to understand. It seems in the first line it is giving ALT section as a "." and in the second bold line it is showing what it is replaced. It would be great if someone can help me sort this out to have a better understand of what each bold line says.

Thanks in advance

chrM 172 . T . 283 . DP=224;AF1=0;AC1=0;DP4=40,182,0,0;MQ=32;FQ=-282 PL 0

chrM 173 . T . 283 . DP=227;VDB=0.0216;AF1=0;AC1=0;DP4=43,175,0,5;MQ=32;FQ=-282;PV4=0.59,1.1e-11,0.28,1 PL 0

chrM 174 . C . 283 . DP=226;AF1=0;AC1=0;DP4=42,183,0,0;MQ=32;FQ=-282 PL 0

chrM 175 . A . 283 . DP=226;AF1=0;AC1=0;DP4=42,182,0,0;MQ=32;FQ=-282 PL 0

chrM 176 . A . 283 . DP=230;AF1=0;AC1=0;DP4=44,185,0,0;MQ=33;FQ=-282 PL 0

chrM 177 . T . 283 . DP=230;AF1=0;AC1=0;DP4=45,182,0,1;MQ=33;FQ=-282;PV4=1,1,0.39,1 PL 0

chrM 178 . A . 283 . DP=227;AF1=0;AC1=0;DP4=43,181,0,0;MQ=32;FQ=-282 PL 0

chrM 178 . ATT . 291 . INDEL;DP=227;VDB=0.0345;AF1=0;AC1=0;DP4=43,170,0,1;MQ=33;FQ=-290;PV4=1,0.37,0.38,0.15 PL 0

chrM 179 . T . 283 . DP=228;VDB=0.0174;AF1=0;AC1=0;DP4=48,172,0,3;MQ=32;FQ=-282;PV4=1,5.3e-09,0.31,0.096 PL 0

chrM 180 . T . 283 . DP=233;VDB=0.0130;AF1=0;AC1=0;DP4=48,180,1,1;MQ=32;FQ=-282;PV4=0.38,3.4e-06,0.34,0.045 PL 0

chrM 181 . A . 283 . DP=235;AF1=0;AC1=0;DP4=46,186,0,0;MQ=32;FQ=-282 PL 0

chrM 182 . C . 283 . DP=236;AF1=0;AC1=0;DP4=49,186,0,0;MQ=33;FQ=-282 PL 0

chrM 183 . A . 283 . DP=243;VDB=0.0143;AF1=0;AC1=0;DP4=50,190,1,1;MQ=33;FQ=-282;PV4=0.38,0.055,1,0.34 PL 0

chrM 184 . G . 283 . DP=244;AF1=0;AC1=0;DP4=51,192,0,0;MQ=33;FQ=-282 PL 0

chrM 185 . G . 283 . DP=244;VDB=0.0153;AF1=0;AC1=0;DP4=50,192,0,0;MQ=33;FQ=-282 PL 0

chrM 186 . C . 283 . DP=243;AF1=0;AC1=0;DP4=51,190,0,0;MQ=33;FQ=-282 PL 0

chrM 3107 . AC A 114 . INDEL;DP=92;VDB=0.0345;AF1=0.5;AC1=1;DP4=12,12,11,20;MQ=32;FQ=117;PV4=0.41,0.0031,1.7e-09,2.6e-05 GT:PL:GQ 0/1:152,0,255:99

mpileup samtools bcftools vcf mpileup • 3.9k views

ADD COMMENT • link updated 9.7 years ago by Biostar 20 • written 12.1 years ago by satish.nair • 0

score 2 · Answer 1 · 2012-04-19

I'm not sure why you have dots in the alt colum, is that becuase you made a .vcf of every single locus? I presume the . in the alt column means that the software doesn't beleive that there's a viable alterante letter. See also base 183. 140 read showing the ref A, 2 reads showing something else. That's not real.

At base 178, you have 233 reads matching the reference, and one with an indel, according to the DP4. So forget that.

The last one is much better looking. 24 reads showing ref letter, 31 showing the alt letter, both directions seen, according to the DP4. The discrepancy between the DP and the DP4 is because the DP includes poor quality reads, and the DP4 doesn't.