Question about discrepancy between VCF file SNPs/INDELs and MutMap output loci

[Biodb-BinLi]

Dear MutMap Team,

Apologies for reaching out during your busy schedule. We encountered an issue where the number of SNPs and indels in mutmap_plot and snp_index.tsv is significantly lower than those in our original VCF file.
Here's the specific context:
I filtered my VCF file using BCFtools with criteria: QUAL < 30 || DP < 15 || GQ < 30. This left 1,743 SNP loci on the chromosome of interest.
I then ran mutplot -v Mutmap_res/30_vcf/mutmap.chr.anno.filtered.vcf -o Mutmap_res/40_mutmap/ --N-bulk 30 --format pdf --igv -S 0 to generate plots.
However, only 13 loci appeared in snp_index.tsv.
We initially suspected built-in filtering during plotting, but the -S 0 parameter should disable this, right? Could you kindly advise on possible causes or solutions? Your expertise would be greatly appreciated.

Best regards,
Bin Li

[YuSugihara]

Hi Bin,

In addition to "-S", there are various filtering parameters, including depth-related options (-d and -D).
Also, the -m option can also have an effect.

The potential reasons could be:
1/ Your sequencing depth across the genome is either too low or too high for the default parameters of -d and -D.
2/ Your bulk sequencing data may have contained one different sample, which caused a lot of SNPs in the VCF, but these were filtered out by our program as noise.

Best,
Yu