René's URL Explorer Experiment

{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"Issues with using the samplot vcf module","articleBody":"Dear Samplot Development Team,\r\n\r\nI would like to express my gratitude for developing such a valuable tool like Samplot. Your efforts have significantly contributed to the research community, and I truly appreciate the hard work you've put into this software.Following that, I've encountered some issues while using the Samplot vcf module that I'd like to discuss with you. I hope you can provide some guidance or solutions to address these concerns.\r\nWhen running the samplot vcf module, there were no errors, but no images were generated. Additionally, when opening the HTML file, it displays 'No data available in table'.My SVs file was generated from 2nd generation 10x resequencing data, processed through Lumpy, Manta, and Delly, and then merged using SURVIVOR. Initially, I executed the following command:\r\n`(py37) [chenzhaojin@lfpara survivor]$ samplot vcf \\\r\n\u003e --filter \"SVTYPE == ‘DEL’ \u0026 SU \u003e= 5\" \\\r\n\u003e --filter \"SVTYPE == 'INV' \u0026 SU \u003e= 3\" \\\r\n\u003e     --vcf filtered_1-30_fixed.vcf \\\r\n\u003e     -d test_1/ \\\r\n\u003e     -O png \\\r\n\u003e     --important_regions bed2.bed\\\r\n\u003e     -b /home/chenzhaojin/expansion/sv/mid75/1-30/delly/alignment_1_sorted.bam \\\r\n\u003e     --sample_ids sample1-30 \u003e samplot_command.sh \r\n(py37) [chenzhaojin@lfpara survivor]$ cd test_1/\r\n(py37) [chenzhaojin@lfpara test_1]$ ll\r\ntotal 1\r\n-rw-r--r-- 1 chenzhaojin lfpara 24507 Oct  9 11:15 index.html`\r\nSubsequently, I reviewed the filtering criteria and attempted to modify the conditions.I discovered that there is an issue with the 'SU' in my VCF file，because my second command produced no output.\r\n`(py37) [chenzhaojin@lfpara survivor]$ grep -v \"^#\" filtered_1-30_fixed.vcf | grep \"SVTYPE=DEL\" | wc -l\r\n747\r\n(py37) [chenzhaojin@lfpara survivor]$ grep -v \"^#\" filtered_1-30_fixed.vcf | grep \"SVTYPE=DEL\" | awk -F';' '{for(i=1;i\u003c=NF;i++) if ($i ~ /SU=/) print $i}' | sort | uniq -c\r\n(py37) [chenzhaojin@lfpara survivor]$ grep -v \"^#\" filtered_1-30_fixed.vcf | grep \"SVTYPE=DEL\" | head -1\r\nNC_010443.5     5537541 MantaDEL:640:0:1:0:0:0  CTTGGATTCCGTCGTGGCAGTGTAACAATCGATAGACATGAGGTTGCGGGTTCGATCTGCCTTGCTCATGGTTAACGATCCGCATGGCGTGAGCTGTGGTAGGTGCAGACGCGGCTCGATCCGAGTTGCTGTGCTCTGGCGTAGGCAGTGCTACAGCTCCGATTCGACCCTAGCCTGGAACTCATATGCCGGAGCGCCAAAAATAGCAAAAAAAAAAAAATAAAAAAAATAACCTTCATACAGAAACTACTAAATAAAAATAGTTAAGACTACAAGTTCAGGAGTTCCCGTCGTGGCGCAGTGGTTAACGAATCCGACTAGAACATGAGGTTGCGGTTCGTCCTGCCTTGCTCAGTGGTTAAGACCGGCGTTGCGTGAGCTGTGGTGTAGGTGCAGACGCGGCTCGGATTCCGCGTTGCTGTGGCTCTGGCGAGGCGTGATACAGCTCGATTCAACCCTAGCTGGAACTCCATATGCGCGGAGCGCCAAGAAATAGCAACAATAACAACAACAGAAAGACAAAAAAAAAAAAAAA     CAGAAACTACTAAATAAAAATAGTT       551     PASS    SUPP=3;SUPP_VEC=111;SVLEN=-449;SVTYPE=DEL;SVMETHOD=SURVIVOR1.0.7;CHR2=NC_010443.5;END=5538075;CIPOS=-1,279;CIEND=-535,10;STRANDS=+-    GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO   ./.:NA:279:0,7:+-:.,.,.,.:DEL,INV,INV,DEL:28:NA:NA:NC_010443.5_5537541-NC_010443.5_5537765,NC_010443.5_5537540-NC_010443.5_5537819,NC_010443.5_5537819-NC_010443.5_5537540,NC_010443.5_5537820-NC_010443.5_5538075      1/1:NA:534:0,19:+-:551,59:DEL,DEL:MantaDEL_640_0_1_0_0_0:CTTGGATTCCGTCGTGGCAGTGTAACAATCGATAGACATGAGGTTGCGGGTTCGATCTGCCTTGCTCATGGTTAACGATCCGCATGGCGTGAGCTGTGGTAGGTGCAGACGCGGCTCGATCCGAGTTGCTGTGCTCTGGCGTAGGCAGTGCTACAGCTCCGATTCGACCCTAGCCTGGAACTCATATGCCGGAGCGCCAAAAATAGCAAAAAAAAAAAAATAAAAAAAATAACCTTCATACAGAAACTACTAAATAAAAATAGTTAAGACTACAAGTTCAGGAGTTCCCGTCGTGGCGCAGTGGTTAACGAATCCGACTAGAACATGAGGTTGCGGTTCGTCCTGCCTTGCTCAGTGGTTAAGACCGGCGTTGCGTGAGCTGTGGTGTAGGTGCAGACGCGGCTCGGATTCCGCGTTGCTGTGGCTCTGGCGAGGCGTGATACAGCTCGATTCAACCCTAGCTGGAACTCCATATGCGCGGAGCGCCAAGAAATAGCAACAATAACAACAACAGAAAGACAAAAAAAAAAAAAAA:CAGAAACTACTAAATAAAAATAGTT:NC_010443.5_5537541-NC_010443.5_5538075,NC_010443.5_5537814-NC_010443.5_5538084 1/1:NA:534:6,5:+-:360,180:DEL,DEL:DEL00000089:NA:NA:NC_010443.5_5537542-NC_010443.5_5538076,NC_010443.5_5537814-NC_010443.5_5538085`\r\nI tried to lower the filtering criteria and instead of using the --filter parameter for filtering, I used the awk command for filtering with su\u003e2. After that, I ran samplot vcf again without specifying the filtering parameter, but it still couldn't generate images or an HTML file with data.\r\n`(py37) [chenzhaojin@lfpara survivor]$ awk -F'\\t' '($0 ~ /^#/ || ($8 ~ /SVTYPE=DEL/ \u0026\u0026 $8 ~ /SUPP=[2-9][0-9]*|SUPP=[1-9][0-9]+/)) {print}' filtered_1-30_fixed.vcf \u003e supp2_1-30_DEL.vcf`\r\n`samplot vcf \\\r\n    --vcf supp2_1-30_DEL.vcf \\\r\n    -d test_2/ \\\r\n    -O png \\\r\n    --important_regions bed2.bed\\\r\n    -b /home/chenzhaojin/expansion/sv/mid75/1-30/delly/alignment_1_sorted.bam \\\r\n    --sample_ids sample1-30 \u003e samplot_command.sh`\r\n`(py37) [chenzhaojin@lfpara survivor]$ cat bed2.bed \r\nNC_010443.5     532       11200`\r\nWhen I use the samplot plot command with my BAM file, it successfully generates images as expected.\r\n`time samplot plot \\\r\n    -n 1-1 1-2 1-30 \\\r\n    -b /home/chenzhaojin/expansion/sv/mid75/1-1/delly/alignment_1_sorted.bam \\\r\n      /home/chenzhaojin/expansion/sv/mid75/1-2/delly/alignment_1_sorted.bam \\\r\n      /home/chenzhaojin/expansion/sv/mid75/1-30/delly/alignment_1_sorted.bam \\\r\n    -o 1_105_274330532.png \\\r\n    -c NC_010443.5 \\\r\n    -s 105 \\\r\n    -e 274330532 \\\r\n    -t DEL`\r\n\r\nThere were no error messages, so I'm at a loss on how to proceed. I would appreciate any assistance or guidance you can provide.","author":{"url":"https://github.com/karen916","@type":"Person","name":"karen916"},"datePublished":"2023-10-09T03:34:56.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":3},"url":"https://github.com/187/samplot/issues/187"}