No InDels

I am running the pipeline on ONT bams generated with minimap2. The SNPs are called but there are no InDels. Why is that?

docker run --ipc=host -v kishwars/pepper_deepvariant:r0.4 run_pepper_margin_deepvariant call_variant -b -f hg19.fa -o pepper_out --ont -r chr22:42520501-42528812 -t 10 -s --phased_output

Deepvariant should call Indels as I have tested it with this data. Is there some option missing for indels?

There are three VCF in the output

HP_OUTPUT, SNP_OUTPUT and name.vcf

it’s not in any of those.

[kishwarshafin]

@husamia ,

We have discussed the issues with the amplicon data. What we would suggest is to add enough flanking regions on both sides of your target sequence so you can capture heterozygous variants that enable phasing of your region of interest. Without the heterozygous variants, it will not be possible for the methods we have developed to be successful in these regions. We are planning to release a backup model for targeted amplicon sequence data. But in this case, where everything is extremely homozygous, our methods will not be able to produce sensible variant calls.

I will close this issue for now and will give you an update once we get to the point where we can officially support targeted sequencing.

[kishwarshafin]

@husamia ,

In this mode, you are running the individual modules of PEPPER-DeepVariant. So, instead of doing allele-likelihood-based candidate-finding with PEPPER-HP, you did a frequency-based candidate finding, where all candidates with allele frequency of 0.10 or higher are reported. Next, you will do variant calling with DeepVariant to get the variants. And finally, you will phase the variants with Margin. This is to see if you get a good set of variants in this region.