默认情况下,sambamba view期望输入文件为 BAM 格式。要使用 SAM 格式的文件,你需要显示指定-S或--sam-input参数,因为sambamba view不会尝试从文件扩展名猜测文件格式。如果遇到不符合 SAM/BAM 规范的标签或字段,sambamba view会跳过这些标签并将无效字段设置为默认值。这意味着即使源文件有些小错误或不规范的地方,工...
使用sambamba去除多重比对/重复/未比对序列 sambamba是高效处理sam/bam文件的工具,sambamba view可以设置一系列条件对我们的比对结果进行过滤,参数如下 其中-F参数可以实现比对结果过滤,使用例子如下 sambamba view -F 'filter expression' example.bam > example.filter.bam filter expression接受and,or,not等逻辑操作符...
/public/home/juncheng/bcbio_install/bin/sambamba view -f bam -L /public/home/juncheng/YHY_WE/work/regions/WGC029878U-noanalysis_blocks.bed /public/home/juncheng/YHY_WE/work/align/WGC029878U/WGC029878U_2015-10-08_YHY_WE1-sort.bam | /public/home/juncheng/bcbio_install/bin/bedtools intersec...
samtools view 04_bam/WTF4.IP.bam|cut-f2,5|sort|uniq-c1137131410214760116301516313163606339089339113550635513393114030640311409164190894191169037701830158313836029960 (3) 用samtools view进行过滤 samtools view -@ 4 -h -b -q 30 -F 4 -F 256 example.bam > example.filtered.bam #去掉比对质量<30,没有比对到参考...
I've got sambamba view running on 149 BAM files on our local scratch server. For the 11 BAM files I'm running that on the supercomputer which I've been attempting to merge the BAM files on. They take up a lot of space, and there isn't enough space on our local server. Running on...
monza:~/tmp$ time ./sambamba view /gnu/data/HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam.orig > /dev/null sambamba 0.6.8-pre3 by Artem Tarasov and Pjotr Prins (C) 2012-2018 LDC 1.11.0 / DMD v2.081.2 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.6)...
gdb -ex 'handle SIGUSR1 SIGUSR2 nostop noprint' \ --args ~/sambamba-test/sambamba-*/bin/sambamba view --throw-error License Sambamba is generously distributed under GNU Public License v2+. Credit Citations are the bread and butter of science. If you are using Sambamba in your research an...