SNiPlay3


StepAnnotation
Step 1: VCFtools Filter
select at runtime
filtered
Unavailable.
Unavailable.
VCF
0.001
0.5
0.0
2
4
All
1
100000000
Step 2: SnpEff
Output dataset 'fileout' from step 1
select at runtime
select at runtime
Step 3: SnpSift Filter
Output dataset 'output' from step 2
(FILTER != 'LowQual')
False
Retain entries that pass filter, remove other entries
Step 4: VCFtools Filter
Output dataset 'output' from step 3
filtered
None
None
VCF
0.001
0.5
0.0
2
2
All
1
100000000
Step 5: VCF to Hapmap
Output dataset 'fileout' from step 4
input
No
Step 6: VCFtools Filter
Output dataset 'fileout' from step 4
filtered
None
None
plink
0.001
0.5
0.0
2
2
SNP
1
100000000
Step 7: VCFtools Stats
Output dataset 'fileout' from step 4
vcf_stats
Step 8: VCF tools SlidingWindow
Output dataset 'fileout' from step 4
snp_density
200000
select at runtime
Step 9: sNMF
Output dataset 'fileout' from step 4
2
5
50
Step 10: SNP density
Output dataset 'fileout' from step 5
200000
densities
Step 11: plink: ped2bed
Output dataset 'fileout' from step 6
Output dataset 'fileout_map' from step 6
Step 12: Ped2Fasta
Output dataset 'fileout' from step 6
filtered
Step 13: MDS plot
Output dataset 'fileout' from step 6
Output dataset 'fileout_map' from step 6
select at runtime

No value found for 'Groups'. Using default: ''.

analyse
Step 14: Readseq
Output dataset 'fileout' from step 12
phylip conversion
12.Phylip|Phylip4
Step 15: FastME
Output dataset 'fileout' from step 14
Newick tree
F84
BIONJ
Step 16: Rooting
Output dataset 'fileout' from step 15
out tree
Step 17: InTreeGreat
Output dataset 'fileout' from step 16
select at runtime

No value found for 'Groups for colorization'. Using default: ''.