{"id":706,"date":"2026-06-24T10:16:47","date_gmt":"2026-06-24T02:16:47","guid":{"rendered":"https:\/\/www.kz-hub.tech\/?p=706"},"modified":"2026-06-24T10:16:47","modified_gmt":"2026-06-24T02:16:47","slug":"%e4%bd%bf%e7%94%a8svaba%e8%bf%9b%e8%a1%8c%e7%bb%93%e6%9e%84%e5%8f%98%e5%bc%82%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"https:\/\/www.kz-hub.tech\/index.php\/2026\/06\/24\/%e4%bd%bf%e7%94%a8svaba%e8%bf%9b%e8%a1%8c%e7%bb%93%e6%9e%84%e5%8f%98%e5%bc%82%e5%88%86%e6%9e%90\/","title":{"rendered":"\u4f7f\u7528SvABA\u8fdb\u884c\u7ed3\u6784\u53d8\u5f02\u5206\u6790"},"content":{"rendered":"

\u5b98\u65b9github: https:\/\/github.com\/walaj\/svaba<\/a>
\nconda \u5b89\u88c5\u540e\u76f4\u63a5\u8fd0\u884c\u5373\u53ef<\/p>\n

\u6784\u5efa\u6279\u91cf\u8fd0\u884c\u811a\u672c\uff1a<\/p>\n

#!\/bin\/bash\n# ============================================================\n# SvABA somatic \u5168\u57fa\u56e0\u7ec4\u6d41\u7a0b \u2014\u2014 \u811a\u672c\u751f\u6210\u547d\u4ee4\n# \u8fd0\u884c\u672c\u6587\u4ef6\u4f1a\u751f\u6210\u53ef\u6267\u884c\u7684 svaba.sh\n# sample_pairs.txt \u683c\u5f0f(tab \u5206\u9694): \u7b2c1\u5217=tumor($a[0])  \u7b2c2\u5217=normal($a[1])\n# \u5728\u6709 ..\/align \u7684\u5de5\u4f5c\u76ee\u5f55\u4e0b\u8fd0\u884c\u751f\u6210\u51fa\u7684 svaba.sh\n#\n# \u4e09\u6b65:\n#   1) svaba run        \u5168\u57fa\u56e0\u7ec4 call(\u4e0d\u52a0 -k,\u5373\u4e0d\u9650\u5236\u67d3\u8272\u4f53)\n#   2) svaba postprocess \u5408\u5e76\/\u6392\u5e8f\/\u53bb\u91cd\/\u5efa\u7d22\u5f15\n#   3) svaba tovcf       \u8f6c\u6210 VCFv4.5\n# \u8f93\u51fa\u524d\u7f00 -a \u7528 tumor \u540d $a[0],\u5404\u6837\u672c\u7ed3\u679c\u843d\u5728\u4ee5 $a[0] \u547d\u540d\u7684\u76ee\u5f55\n# ============================================================\n\nREF=\/home\/zhoukaiwen\/database\/GRCh38\/genecode_GRCh38.p14.genome.fa\nBLACKLIST=\/home\/zhoukaiwen\/database\/gridss\/ENCFF356LFX.bed\nTHREADS=8\n\nperl -ne 'chomp;next if \/^$\/;@a=split\/\\t\/;\n$ref="\/home\/zhoukaiwen\/database\/GRCh38\/genecode_GRCh38.p14.genome.fa";\n$bl="\/home\/zhoukaiwen\/database\/gridss\/ENCFF356LFX.bed";\n$t=8;\nprint "mkdir -p $a[0] && cd $a[0] && svaba run -t ..\/..\/align\/$a[0]_bqsr.bam -n ..\/..\/align\/$a[1]_bqsr.bam -G $ref -a $a[0] -p $t --blacklist $bl > $a[0].run.log 2>&1 && svaba postprocess -i $a[0] -t $t -m 32G >> $a[0].run.log 2>&1 && svaba tovcf -i $a[0].bps.sorted.dedup.txt.gz -b ..\/..\/align\/$a[0]_bqsr.bam -a $a[0] >> $a[0].run.log 2>&1 && echo $a[0] svaba ok\\n";\n' sample_pairs.txt > svaba.sh<\/code><\/pre>\n
\u751f\u6210\u6587\u4ef6\u53c2\u8003\uff1a<\/p>\n
mkdir -p FETB06-BLPT-E && cd FETB06-BLPT-E && svaba run -t ..\/..\/align\/FETB06-BLPT-E_bqsr.bam -n ..\/..\/align\/FETB06-N_bqsr.bam -G \/home\/zhoukaiwen\/database\/GRCh38\/genecode_GRCh38.p14.genome.fa -a FETB06-BLPT-E -p 8 --blacklist \/home\/zhoukaiwen\/database\/gridss\/ENCFF356LFX.bed > FETB06-BLPT-E.run.log 2>&1 && svaba postprocess -i FETB06-BLPT-E -t 8 -m 32G >> FETB06-BLPT-E.run.log 2>&1 && svaba tovcf -i FETB06-BLPT-E.bps.sorted.dedup.txt.gz -b ..\/..\/align\/FETB06-BLPT-E_bqsr.bam -a FETB06-BLPT-E >> FETB06-BLPT-E.run.log 2>&1 && echo FETB06-BLPT-E svaba ok\nmkdir -p FETB06-BLPT-M && cd FETB06-BLPT-M && svaba run -t ..\/..\/align\/FETB06-BLPT-M_bqsr.bam -n ..\/..\/align\/FETB06-N_bqsr.bam -G \/home\/zhoukaiwen\/database\/GRCh38\/genecode_GRCh38.p14.genome.fa -a FETB06-BLPT-M -p 8 --blacklist \/home\/zhoukaiwen\/database\/gridss\/ENCFF356LFX.bed > FETB06-BLPT-M.run.log 2>&1 && svaba postprocess -i FETB06-BLPT-M -t 8 -m 32G >> FETB06-BLPT-M.run.log 2>&1 && svaba tovcf -i FETB06-BLPT-M.bps.sorted.dedup.txt.gz -b ..\/..\/align\/FETB06-BLPT-M_bqsr.bam -a FETB06-BLPT-M >> FETB06-BLPT-M.run.log 2>&1 && echo FETB06-BLPT-M svaba ok\nmkdir -p FETB06-FA-OL-E && cd FETB06-FA-OL-E && svaba run -t ..\/..\/align\/FETB06-FA-OL-E_bqsr.bam -n ..\/..\/align\/FETB06-N_bqsr.bam -G \/home\/zhoukaiwen\/database\/GRCh38\/genecode_GRCh38.p14.genome.fa -a FETB06-FA-OL-E -p 8 --blacklist \/home\/zhoukaiwen\/database\/gridss\/ENCFF356LFX.bed > FETB06-FA-OL-E.run.log 2>&1 && svaba postprocess -i FETB06-FA-OL-E -t 8 -m 32G >> FETB06-FA-OL-E.run.log 2>&1 && svaba tovcf -i FETB06-FA-OL-E.bps.sorted.dedup.txt.gz -b ..\/..\/align\/FETB06-FA-OL-E_bqsr.bam -a FETB06-FA-OL-E >> FETB06-FA-OL-E.run.log 2>&1 && echo FETB06-FA-OL-E svaba ok<\/code><\/pre>\n
\u7528\u4e8e\u63d0\u4ea4sbatch\u7684\u811a\u672c\uff1a<\/p>\n
#!\/bin\/bash\n#SBATCH -J svaba\n#SBATCH -N 1\n#SBATCH -n 1\n#SBATCH -c 8\n#SBATCH --mem=32G\n#SBATCH --array=1-59%30\n#SBATCH -o slurm_log\/svaba_%A_%a.out\n#SBATCH -e slurm_log\/svaba_%A_%a.err\n\n# \u6309\u884c\u53d6\u51fa svaba.sh \u4e2d\u7684\u547d\u4ee4(\u6bcf\u884c\u4e00\u4e2a\u6837\u672c)\nCMD=$(sed -n "${SLURM_ARRAY_TASK_ID}p" svaba.sh)\n\necho "================================================="\necho "JobID      : $SLURM_JOB_ID"\necho "Array Task : $SLURM_ARRAY_TASK_ID"\necho "Command    : $CMD"\necho "Start Time : $(date)"\necho "================================================="\n\neval "$CMD"\n\necho "Finished : $(date)"<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"
\u5b98\u65b9github: https:\/\/github.com\/walaj\/svaba conda \u5b89\u88c5\u540e\u76f4\u63a5\u8fd0\u884c\u5373…<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-706","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/706","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/comments?post=706"}],"version-history":[{"count":1,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/706\/revisions"}],"predecessor-version":[{"id":707,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/706\/revisions\/707"}],"wp:attachment":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/media?parent=706"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/categories?post=706"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/tags?post=706"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}