Question: venn diagram for multiple vcf files
0
gravatar for syedahamdani94
11 months ago by
syedahamdani940 wrote:

Hi everyone! i am trying to make venn diagram containing both common and unique variants through VcfToolz but getting unique variants in output venn diagram, common variants are missing may be due to different quality and depth values. if i try to give it vcf files with first five columns only e.g., #CHROM POS ID REF ALT, It gives following error

Traceback (most recent call last):
File "/home/ngs/.local/bin/vcftoolz", line 11, in
sys.exit(main())
File "/home/ngs/.local/lib/python2.7/site-packages/vcftoolz/cli.py", line 223, in main
return args.func(args) # this executes the function previously associated with the subparser with set_defaults
File "/home/ngs/.local/lib/python2.7/site-packages/vcftoolz/cli.py", line 121, in compare_command
vcftoolz.compare(args.truth_flag, vcf_path_list, args.exclude_snps, args.exclude_indels, args.exclude_vars, args.exclude_refs, args.exclude_hetero, args.exclude_filtered, args.exclude_missing, args.table_file)
File "/home/ngs/.local/lib/python2.7/site-packages/vcftoolz/vcftoolz.py", line 505, in compare
sample_snps_list = [get_snp_list(truth_flag, path, *packed_exclude_flags) for path in vcf_path_list] # List of SampleSnps
File "/home/ngs/.local/lib/python2.7/site-packages/vcftoolz/vcftoolz.py", line 272, in get_snp_list
for record, call in call_generator(input, exclude_snps, exclude_indels, exclude_vars, exclude_refs, exclude_hetero, exclude_filtered, exclude_missing):
File "/home/ngs/.local/lib/python2.7/site-packages/vcftoolz/vcf_call_parser.py", line 586, in call_generator
for record in reader:
File "/home/ngs/.local/lib/python2.7/site-packages/vcf/parser.py", line 547, in next
pos = int(row[1])
IndexError: list index out of range
**tried both commands for making venn diagrams**
**$ vcftoolz compare --exclude_ref --exclude_missing --exclude_filtered  ERR759314_filt.vcf ERR1395564-filt.vcf ERR757814_filt.vcf ERR759307_filt.vcf > summary-exclude-ref.txt
$ vcftoolz compare ERR759314_filt.vcf ERR1395564-filt.vcf ERR757814_filt.vcf ERR759307_filt.vcf > summary.txt**

your suggestions will be really appreciated

ADD COMMENTlink modified 11 months ago by lieven.sterck8.5k • written 11 months ago by syedahamdani940

Please consider editing your tags. People use tags to search for questions they might be able to answer. Replicating the question as a single tag is not helpful. Consider breaking up into single words or phrases.

ADD REPLYlink written 11 months ago by Emily_Ensembl21k
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