Hi Dave,
I try to genotype around 1.7k samples with svtools. lsort worked but, I can not do lmerge step.
I keep having this following error:
Traceback (most recent call last):
File "/home/zhiyan/.conda/envs/AGAT/bin/svtools", line 10, in
sys.exit(main())
File "/home/zhiyan/.conda/envs/AGAT/lib/python2.7/site-packages/svtools/cli.py", line 79, in main
sys.exit(args.entry_point(args))
File "/home/zhiyan/.conda/envs/AGAT/lib/python2.7/site-packages/svtools/lmerge.py", line 638, in run_from_args
weighting_scheme=args.weighting_scheme)
File "/home/zhiyan/.conda/envs/AGAT/lib/python2.7/site-packages/svtools/lmerge.py", line 601, in l_cluster_by_line
v_id = r_cluster(BP_l, sample_order, v_id, use_product, vcf, vcf_out, include_genotypes, weighting_scheme)
File "/home/zhiyan/.conda/envs/AGAT/lib/python2.7/site-packages/svtools/lmerge.py", line 532, in r_cluster
v_id = merge(BP_r, sample_order, v_id, use_product, vcf, vcf_out, include_genotypes, weighting_scheme)
File "/home/zhiyan/.conda/envs/AGAT/lib/python2.7/site-packages/svtools/lmerge.py", line 507, in merge
var=create_merged_variant(BP, cliq, v_id, vcf, use_product, weighting_scheme)
File "/home/zhiyan/.conda/envs/AGAT/lib/python2.7/site-packages/svtools/lmerge.py", line 242, in create_merged_variant
max_i_R = p_R.index(max(p_R))
ValueError: max() arg is an empty sequence
I have run several individual without any issues，but there were issues with these 1.7k samples.
If you can give me any idea to solve this problem, it would be awesome.
Best,
Jason Hoo
hall-lab
