which tool should be used to call the genotype?

Question

[JENNIE]

Hello! I am trying to call germline mutation (genotype) from our fastq file.

 ref  atgcgt*T*cgtaaa

  #1  atgcgt*A*cgtaaa   only      -> genotype of #1 is homozygous allele AA

  #2  atgcgt*T*cgtaaa             -> genotype of #2 is heterozygous allele TA

      atgcgt*A*cgtaaa

In this case, which tool should be used to call the variant?

Is this possible with mutect or haplotypecaller?

Thanks.

[Friederike]

mutect and haplotypecaller are tools for identifying reference and alternative alleles, yes.

Your question is lacking context (e.g. did you sequence a single gene or entire genomes? how many samples do you have? what is the ultimate goal of the analysis? have you tried (and possibly failed) specific tools already? and so on), so replies will probably be not as helpful as they could be given the proper background information.

[JENNIE]

Thank you for answer. We performed NGS for the library amplified by the target enrichment method and analyzed 100 samples. Through this analysis, we aim to detect the genotype observed at a specific SNP position.

The HaplotypeCaller detects the variant (a base different from the reference), but does not discovery the same base as the reference. so it seems that I should find the variant with position-based method. Is position-based variant discovery possible using haplotypecaller?

[desouzareis.r]

Since you would like to call germline mutation, you should use the HaplotypeCaller. The HaplotypeCaller with -ERC BP_RESOLUTION would give you per base call (base different from the reference or the same base as the reference).