search

hall-lab / svtyper

Bayesian genotyper for structural variants
MIT License
125 stars 55 forks source link

SVtyper on lumpy traditional vcf #121

Closed nitinra closed 3 years ago

nitinra commented 3 years ago

Hi all, I am trying to run svtyper from vcf files from lumpy. I have followed the tutorial posted on the lumpy github to produce the vcf. This is the error I am getting while using svtyper:

<Warning: --split_bam (-S) is deprecated. Ignoring GC1601.splitters.bam. Traceback (most recent call last): File "/work/nitinr/svtyper2_env/bin/svtyper", line 11, in load_entry_point('svtyper==0.7.1', 'console_scripts', 'svtyper')() File "/work/nitinr/svtyper2_env/lib/python2.7/site-packages/svtyper/classic.py", line 575, in cli sys.exit(main()) File "/work/nitinr/svtyper2_env/lib/python2.7/site-packages/svtyper/classic.py", line 568, in main args.max_ci_dist) File "/work/nitinr/svtyper2_env/lib/python2.7/site-packages/svtyper/classic.py", line 150, in sv_genotype sample = Sample.from_bam(bam_list[i], num_samp, min_lib_prevalence) File "/work/nitinr/svtyper2_env/lib/python2.7/site-packages/svtyper/parsers.py", line 665, in from_bam name = bam.header['RG'][0]['SM'] File "pysam/libcalignmentfile.pyx", line 547, in pysam.libcalignmentfile.AlignmentHeader.getitem KeyError: 'RG'>

Huangwenxuan666888 commented 2 months ago

Hi, I encountered the same issue; did you manage to resolve it in the end?