I was trying to use samplot on my various call sets; however, for Pindel, all of the variants are homref so I and was directed here.
A couple of my call sets are throwing errors with svtyper
Set up environment and install svtyper
cd ~/bin
virtualenv svtyper
source svtyper/bin/activate
pip install git+https://github.com/hall-lab/svtyper.git
cd ~/celegans
Run svtyper
svtyper -i Pindelvcf \
-B 470.sorted.dedupped.bam \
-l 470.sorted.dedupped.bam.json > Pindel.gt.vcf
Traceback (most recent call last):
File "/home/mtg/bin/svtyper/bin/svtyper", line 8, in <module>
sys.exit(cli())
File "/home/mtg/bin/svtyper/local/lib/python2.7/site-packages/svtyper/classic.py", line 575, in cli
sys.exit(main())
File "/home/mtg/bin/svtyper/local/lib/python2.7/site-packages/svtyper/classic.py", line 568, in main
args.max_ci_dist)
File "/home/mtg/bin/svtyper/local/lib/python2.7/site-packages/svtyper/classic.py", line 265, in sv_genotype
ciA = confidence_interval(var, 'CIPOS', 'CIPOS95', max_ci_dist)
File "/home/mtg/bin/svtyper/local/lib/python2.7/site-packages/svtyper/parsers.py", line 12, in confidence_interval
ci = map(int, var.info[tag].split(','))
KeyError: 'CIPOS'
svtyper -i Delly.vcf \
-B 470.sorted.dedupped.bam \
-l 470.sorted.dedupped.bam.json > Delly.gt.vcf
Warning: Unsupported SVTYPE at variant INS00000073 (INS). Skipping.
Traceback (most recent call last):
File "/home/mtg/bin/svtyper/bin/svtyper", line 8, in <module>
sys.exit(cli())
File "/home/mtg/bin/svtyper/local/lib/python2.7/site-packages/svtyper/classic.py", line 575, in cli
sys.exit(main())
File "/home/mtg/bin/svtyper/local/lib/python2.7/site-packages/svtyper/classic.py", line 568, in main
args.max_ci_dist)
File "/home/mtg/bin/svtyper/local/lib/python2.7/site-packages/svtyper/classic.py", line 234, in sv_genotype
if var.info['MATEID'] in breakend_dict:
KeyError: 'MATEID'
svtyper -i gridss.vcf \
-B 470.sorted.dedupped.bam \
-l 470.sorted.dedupped.bam.json > gridss.gt.vcf
Traceback (most recent call last):
File "/home/mtg/bin/svtyper/bin/svtyper", line 8, in <module>
sys.exit(cli())
File "/home/mtg/bin/svtyper/local/lib/python2.7/site-packages/svtyper/classic.py", line 575, in cli
sys.exit(main())
File "/home/mtg/bin/svtyper/local/lib/python2.7/site-packages/svtyper/classic.py", line 568, in main
args.max_ci_dist)
File "/home/mtg/bin/svtyper/local/lib/python2.7/site-packages/svtyper/classic.py", line 234, in sv_genotype
if var.info['MATEID'] in breakend_dict:
KeyError: 'MATEID'
svtyper -i manta_candidateSV.vcf \
-B 470.sorted.dedupped.bam \
-l 470.sorted.dedupped.bam.json > manta_candidateSV.gt.vcf
Traceback (most recent call last):
File "/home/mtg/bin/svtyper/bin/svtyper", line 8, in <module>
sys.exit(cli())
File "/home/mtg/bin/svtyper/local/lib/python2.7/site-packages/svtyper/classic.py", line 575, in cli
sys.exit(main())
File "/home/mtg/bin/svtyper/local/lib/python2.7/site-packages/svtyper/classic.py", line 568, in main
args.max_ci_dist)
File "/home/mtg/bin/svtyper/local/lib/python2.7/site-packages/svtyper/classic.py", line 266, in sv_genotype
ciB = confidence_interval(var, 'CIEND', 'CIEND95', max_ci_dist)
File "/home/mtg/bin/svtyper/local/lib/python2.7/site-packages/svtyper/parsers.py", line 12, in confidence_interval
ci = map(int, var.info[tag].split(','))
KeyError: 'CIEND'
Following the troubleshooting section I used lib_stats.R script to produce the insert size histograms from the JSON file. Here it is:
I was trying to use
samplot
on my various call sets; however, for Pindel, all of the variants are homref so I and was directed here.A couple of my call sets are throwing errors with
svtyper
Set up environment and install svtyper
Run svtyper
Following the troubleshooting section I used
lib_stats.R
script to produce the insert size histograms from the JSON file. Here it is:470.json.pdf
Any idea what the problem could be?