somatic short variant calling from patients having autoimmune disease

Question

[Mehmet]

Dear all,

I have been asked to perform variant calling (somatic short variant calling) from around 50 patines who have an autoimmune disease. There is no normal/control samples. only samples from blood.

I was digging a appropriate approach/tool to perform this task, but I am confused at some points.(which were partly covered at various forums including biostar).

I would like to get suggestions on;

gatk2 mutect2, also some topics from biostar, says tumor and normal samples should be induced into the analyses. but my samples are not from tumor samples.

I was wondering how to proceed with my own data without normal samples.

[Cyriac Kandoth]

This sounds like an interesting project. Is this DNA-seq on whole blood, or T-cell receptor sequencing? If the former, then you're more likely to just detect clonal hematopoiesis mutations.

[Mehmet]

Yes, it is getting more interesting. This is DNA-seq on whole blood.

Answer 1

[ATpoint]

In this context you can replace "tumor" by "case" so case versus control. Yes, if you are interested in somatic mutations in a certain tissue then a matched normal control would have been a good idea. Alternatively you can call variants on the data you have and then check the variants against existing databases such as dbSNP or 1000Genomes or TOPMED to see what the VAFs are in other datasets/populations. That then can give some idea whether the variant is rather common or rather unique for that disease. For the entire variant calling process you could use e.g. the Sarek workflow from nf-core, see https://github.com/nf-core/sarek