clustered snps can't be merged by scylla

[ShannonDaddy]

Hi, I found that some clustered snps can't be merged by scylla. I don't see why. Attached is my igv snapshot, bam files and scylla options.

ScyllaLogs.zip
igv_snpshot.zip
bam_files.zip

I need some help, thanks!

[tamsen]

Hi there,

So from your Scylla log it says
"6/30/20 4:15 PM 1 Neighborhood building complete. 0 neighborhoods created." which means exactly 0 variants were found that can be used to build phasing neighborhoods. Either all your variants failed filters (unlikely, but check your vcf, do they pass?), or it cant find them for some other reason, like it thinks they are outside of the intervals you care about.

In your ScyllaOptions.used.json, it says
"PhasableVariantCriteria": {
"PassingVariantsOnly": true,
"HetVariantsOnly": false,
"PhasingDistance": 30,
"ChrToProcessArray": [],
"FilteredNbhdToProcess": null,
"MaxNumNbhdsToProcess": -1
},

So, from the options used, its only going to phase passing variants. The fact that ChrToProcessArray is empty is a bit worrying. Try explicitly telling it what chr you want to use, or submit an interval/bed file along with it. I forget exactly which arguments, but hopefully running the scylla help command will tell you. Also, your chromosome names in your bam, genome, and vcf all have to match up. Hope this can get you unstuck!

best
Tamsen

[ShannonDaddy]

Hi there,

So from your Scylla log it says
"6/30/20 4:15 PM 1 Neighborhood building complete. 0 neighborhoods created." which means exactly 0 variants were found that can be used to build phasing neighborhoods. Either all your variants failed filters (unlikely, but check your vcf, do they pass?), or it cant find them for some other reason, like it thinks they are outside of the intervals you care about.

In your ScyllaOptions.used.json, it says
"PhasableVariantCriteria": {
"PassingVariantsOnly": true,
"HetVariantsOnly": false,
"PhasingDistance": 30,
"ChrToProcessArray": [],
"FilteredNbhdToProcess": null,
"MaxNumNbhdsToProcess": -1
},

So, from the options used, its only going to phase passing variants. The fact that ChrToProcessArray is empty is a bit worrying. Try explicitly telling it what chr you want to use, or submit an interval/bed file along with it. I forget exactly which arguments, but hopefully running the scylla help command will tell you. Also, your chromosome names in your bam, genome, and vcf all have to match up. Hope this can get you unstuck!

best
Tamsen

Thanks， I'll check the arguments again.