DiscoSNP-RAD: using 1SNP_by_cluster.py

Question

[jomare1188]

Hello i'm trying DiscoSnp++ and succesfully ran run_discoSnpRad.sh and discoRAD_finalization.sh. Since i'll use Structure i only need one SNP per locus, but it seems 1SNP_by_cluster.py doesn't ran with filter_paralogs.py called by discoRAD_finalization.sh (as explain in the header of 1SNP_by_cluster.py) wrapper, so i tried to run 1SNP_by_cluster.py manually but it filters out all the SNPs as follows

python3 1SNP_by_cluster.py discoRad_MslI_k_31_c_20_D_10_P_5_m_0_coherent_sorted_with_clusters.vcf
nb SNP before : 158261
nb SNP after  : 0

How can i make sure discoRAD_finalization.sh ran filter_paralogs.py and 1SNP_by_cluster.py ? how can i run 1SNP_by_cluster.py manually?

[Gio12]

I am also having this same problem. Please let me know if you find a solution to this issue. Thank you in advance!

Sincerely, Gio

Answer 1

[jomare1188]

i solved this problem, i don't know really what it was but...

• i updated the las version of discoRAD_finalization.sh (11 days ago) https://github.com/GATB/DiscoSnp/blob/master/scripts_RAD/discoRAD_finalization.sh

*i configured run_discoSnpRad.sh to run the full pipe line without call explicitly discoRAD_finalization.sh

it seems the variants didn't clusterize properly (only one cluster called cluser_-1_size_1 in .vcf) and so 1SNP_by_cluster.py could't work