Genotyping

Question

[kiran]

Hello guys,

I'm very much in need of getting clarity to this doubt, please open a discussion regarding this.

I'm dealing with Genotyping tools which takes input files as aligned .Bam files and .Fasta(reference genome file) and gives the variant call.

My doubt:

Every genotyping tool is actually realigning the reads before calling a variant, but i want to know how is genotyping tool picking the reads to realign and how can we know which reads have realigned and what machanism they have used to realign. like (bowtie2 and bwa mem processes).

thanks for your time, really appreciate your time.

best regards, kiran.

[LChart]

I'm not sure how often realignment is used specifically any longer; many callers are using local assembly. The assembled haplotypes are then compared to the local reference sequence (divergent events will be anchored on both sizes by homozygous reference sequences) to establish a parsimonious representation of the events.

bcftools mpileup uses base alignment quality (10.1093/bioinformatics/btr076) as a quality score adjustment for potentially problematic local alignments; but does not attempt to re-align reads locally.

See https://qcb.ucla.edu/wp-content/uploads/sites/14/2016/03/GATKwr12-3-IndelRealignment.pdf

[kiran]

thank you so much, i will look into local assembly and also the link provided.

Actually i'm using tandem repeats genotyping tool, called GangSTR.