Tool to do Variant calling from contigs data
Hello ! I have contigs data in FASTA format that I have downloaded from PATRIC database. I would like to spot SNPs/Indels in those sequences. As I am quite new in this domain and I don't really know which tool or protocol to use. So if you have any advice... :)
Thank you for your help !
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de.mecquenem.ninon •
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My apology, this is no answer, but I'm curious and would love to know available solutions as well. The best a quick search yielded is Heng Li's fermikit. Maybe you can skip the assembly stage and feed it the assemblies?
The Fermikit works very well. It's still not made for contigs/supoercontigs data, but it looks like a serious tool and I have the good VCF format output ! Thank you for your help !
For now I am trying a BWA-MEM (to get bam files) then GATK (haplotypeCaller). But it does not work very well (Error messages while running HaplotypeCaller), and I am not even sure it is the best protocol in this case. I'll have a look on fermikit, thank you very much !
Hi de.mecquenem.ninon,
This reply is better suited as a comment on Carambakaracho's answer. Answers should ONLY be used to respond to the original question at the top of this page. I moved your post to a comment. But as you see this is not perfect.
fin swimmer
Deeply sorry, it was my first post and I havn't noticed the different ways of answering... Thank you for your answer !
Hello,
I don't know whether the restriction mentioned in this post still exists. So be careful.
fin swimmer
Variant calling without much effort can be done with Freebayes although you need to filter for false positive calls(vcffilter step). However, as a start, it is best to go through the best practices offered by GATK since pre-processing makes a huge difference.