How to Call Genotypes on NGS datasets for linkage

[krawitz]

Hi there,
there are several decent variant callers for NGS data sets, such as samtools, GATK, ... that report variants to a reference in vcf4.0 format. These are well suited for variant detection.
Now let's suppose I want to call genotypes (not only variants) on a NGS dataset, that will be used for linkage analysis. Then I am not only interested in sequence variants, but also genotypes, that agree with the reference at certain positions.
samtools allows to call variants at certain positions with the -l list option. But how do I get the info that the genotype is identical to the reference? So basically I wonder, whether the following line in vcf format would make sense or is allowed:

#chr pos id ref alt qal
20 14370 rs6054257 G G 29

Any suggestions?

cheers,

peter

[krawitz]

The following options in samtools will call genotypes even, if they agree with the reference:
samtools mpileup -f <ref.fa> -l <PositionsToGenotype> -cg <alignment.bam> >genotypes.bcf
bcftools view genotypes.bcf -g > genotypes.vcf

samtools reports a position that agree with the reference as:
#chr pos ID ref alt
chr10 1023909 . A .

I didn't find this specification in the vcf format description, but it seems rather intuitive.

hope this helps,
peter

[vyellapa]

The following options in samtools will call genotypes even, if they agree with the reference:
samtools mpileup -f <ref.fa> -l <PositionsToGenotype> -cg <alignment.bam> >genotypes.bcf
bcftools view genotypes.bcf -g > genotypes.vcf

samtools reports a position that agree with the reference as:
#chr pos ID ref alt
chr10 1023909 . A .

I didn't find this specification in the vcf format description, but it seems rather intuitive.

hope this helps,
peter

I'm curious how you would differentiate an indel from a . that corresponds to alt allele that is the same as the reference allele?