How to know homozygous or heterozygous in samtools results

[maivantan]

Dear All,
I run samtools and got results. But i don't know how to identify which SNP is homozygous for either parent or heterozygous
any suggestion please

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT wrc20014.sorted.bam.bam
chr01 27400 . N G 68 . DP=22;VDB=3.856020e-04;AF1=1;AC1=2;DP4=0,0,0,8;MQ=29;FQ=-51 GT:PL:GQ 1/1:101,24,0:45
chr01 27401 . N C,G 75 . DP=22;VDB=1.934810e-04;AF1=1;AC1=2;DP4=0,0,0,9;MQ=28;FQ=-51 GT:PL:GQ 1/1:108,24,0,104,10,101:45

[donfreed]

Hi maivantan,

You can tell the both the variants are homozygous from the genotype (GT) field in the 10th column.

1/1:101,24,0:45

The 1/1 indicates a homozygous variant.
0/1 would indicate a heterozygous variant.

Both of the variants in your post are homozygous.

Here is the VCF format specification for reference:

http://samtools.github.io/hts-specs/VCFv4.2.pdf

[maivantan]

Thank you very much Donfreed,

[maivantan]

Dear don freed,
I sequenced F2 population, and got the result, i posted here a part of it

0/1:71,0,171:74
0/1:155,0,160:99
0/1:113,0,193:99
0/1:69,0,139:72
1/1:203,90,0:99

1/1:113,199,0:99
1/1:113,199,0:99

all my data showed 0/1 or 1/1. I know 0/1 is heterozygous, 1/1 is homozygous
my question is what is homozygous for parent 1 and what is homozygous for parent 2?
which command should i add to know about that?

Thank you very much

[TiborNagy]

Dear maivantan,

There is no such information in the VCF file. You need to sequence the parents.

[maivantan]

Dear TiborNagy,

it means that i have to sequence parent1, parent2 and F2 population, then compare to detect polymorphic SNPs, right?

i would like to ask you how can I export the data to excel file, just copy and past?

Thank you very much

[TiborNagy]

Dear TiborNagy,
it means that i have to sequence parent1, parent2 and F2 population, then compare to detect polymorphic SNPs, right?

Right.

I do not know what is Excell
But import as text and use TAB as field separator.

[maivantan]

Thank you very much TiborNagy,

[swbarnes2]

Dear All,
I run samtools and got results. But i don't know how to identify which SNP is homozygous for either parent or heterozygous
any suggestion please

Yes, yes you did.

But are you sure that those results make sense? Samtools should be telling you what the reference letter is at each point, but in your output, they are all N's. I suggest you search this site for when other people have had that problem, and attempt to fix that.

That problem is why you have no 0/0 results; if your reference letters are all N's, you will never have homozygous matches.