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
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
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