René's URL Explorer Experiment

{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"svtype = variant.info.get(\"SVTYPE\", \"SV\")","articleBody":"I am getting the following error and I am not sure how to go around this. I used the following command to annotate the my vcf.\r\n\r\n`duphold -v macope2_sorted.vcf -b ../macOpe2.sorted.bam -f /data/okendojo/datashare/macOpeProject/macOpe2Assembly.fasta -t 24 -o mc.vcf` but I cannot get the SVTYPE column information.\r\n\r\n```\r\n(samplot) [okendojo@cn0798 bcgFile]$ samplot vcf --vcf mc.vcf  -d test -O png -b ../macOpe2.sorted.bam \r\nTraceback (most recent call last):\r\n  File \"/vf/users/okendojo/conda/envs/samplot/bin/samplot\", line 10, in \u003cmodule\u003e\r\n    sys.exit(main())\r\n  File \"/vf/users/okendojo/conda/envs/samplot/lib/python3.10/site-packages/samplot/__main__.py\", line 31, in main\r\n    args.func(parser, args, extra_args)\r\n  File \"/vf/users/okendojo/conda/envs/samplot/lib/python3.10/site-packages/samplot/samplot_vcf.py\", line 1133, in vcf\r\n    commands, table_data = generate_commands(\r\n  File \"/vf/users/okendojo/conda/envs/samplot/lib/python3.10/site-packages/samplot/samplot_vcf.py\", line 949, in generate_commands\r\n    svtype = variant.info.get(\"SVTYPE\", \"SV\")\r\n  File \"pysam/libcbcf.pyx\", line 2711, in pysam.libcbcf.VariantRecordInfo.get\r\nValueError: Invalid header\r\n```","author":{"url":"https://github.com/okendojo","@type":"Person","name":"okendojo"},"datePublished":"2023-05-26T18:36:33.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":6},"url":"https://github.com/181/samplot/issues/181"}