I did a samtools pileup and ended in a vcf format which is confuses at INDEL's

[ssn4ssn]

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

[tonybolger]

Given the DP4 and PL numbers, it doesn't look like there are any variants here except for the last line, where a C has been dropped (and it looks hetrozygous).

BTW, normally bcftools doesn't show non-variants when using -v. Something is strange.