variant_analysis

basic scripts to perform small variant analysis on a server

Read mapping

BWA mem for read mapping

Variant calling

Several alternatives for variant calling

We aimed at producing gVCF data or call all genomes simultaneously in order to handle Ref-calls (same as reference genome) and No-calls (no read support) and obtain a better multigenome dataset. It is also possible to call each genome to VCF and merge the VCF files but doing so the No-calls will be represented as Ref-calls which is not good and is what we get below with freebayes-parallel.

classical bcftools calling

NOTE: We use here bcftools mpileup (with new arguments) rather than the old samtools mpileup syntax used in older tutorials.

GATK4 best ptractice (very slow single core steps)

elPrep5 GATK4 accellerated alternative (developped for human genomes)

Google deepvariant alternative (very popular)

freebayes alternative (parallel version used here for speedup)

NOTE: Freebayes is used here as it is a very poular tool. However freebayes does not (yet) seem to produce gVCF to a level comparable to other tools, we are therefore producing separate VCF files here and merging them with bcftools. A particular issue is when a variant in one genome is a SNV while an indel is present in another genome. In such case, merging will not reflect the complexity of the situation and might lead to call issues.

Variant annotation and filtering

SNPEFF for variant annotation and SNPSIFT for filtering