报错信息 Forward and reverse reads not paired. Check that BAM files have the samereadnames and are sorted. 分析 提示是没有排序或者R1、R2没有配对,手动sort再分步运行HiC-Pro samtools sort -@10-n -m10G -T temp1 xxxR1.bam> xxxR1.sort.bam samtools sort -@10-n -m10G -T temp2 xxxR2....
如果t.1.merge.subreads.bam文件存在,你可以使用samtools index命令来为其建立索引。索引文件将允许更快速地访问BAM文件中的特定区域。执行以下命令: bash samtools index t.1.merge.subreads.bam 这条命令将生成一个名为t.1.merge.subreads.bam.bai的索引文件。 验证索引文件t.1.merge.subreads.bam.bai是否...
Showing 5 changed files with 37 additions and 4 deletions. Whitespace Ignore whitespace Split Unified bam_sort.c test merge test_template_coordinate.1.sam test_template_coordinate.2.sam test_template_coordinate.expected.sam test.pl ...
Turn into BAM files, $ ./samtools view -S -b empty.sam > empty.bam $ ./samtools view -S -b example.sam > example.bam $ ./samtools view -h example.sam @SQ SN:1 LN:239940 @PG ID:bwa PN:bwa VN:0.6.2-r126 HWI-1KL120:88:D0LRBACXX:1:1101:1780:2146 77 * 0 0 * * 0 ...
filter=suffix('.sort.dedup.realn.recal.bam'), output='.raw.snps.indels.g.vcf')# Combine G.VCF files for all samples using GATKpipeline.merge(#...这里部分代码省略... 开发者ID:bjpop,项目名称:complexo_pipeline,代码行数:103,代码来源:pipeline.py 示例9: only ▲点...
bam_producer_command | samtools view -h | mergesam.py -o output.bam Specifying a reference If the sam files have no headers, you'll need a reference: mergesam.py -o output.bam input.bam -r reference.fa.fai You can also supply the name of a fasta file, in which case the fasta in...
The two BAM files must be sorted by name before using ban-mergeRef. You can use samtools sort (http://www.htslib.org/doc/samtools.html) to sort your BAM files with the option -n. Example of command line bam-mergeRef -a <reference name 1> -b <reference name 2> -t [trashfile...
($bDebug || $bVerbose) ? print STDERR "\nMerging bam files ...\n" : ();if (! (defined $hCmdLineOption{'samtools_bin_dir'}) ) { $hCmdLineOption{'samtools_bin_dir'} = SAMTOOLS_BIN_DIR; }$sCmd = $hCmdLineOption{'samtools_bin_dir'}."/samtools merge". " ...
Automate common sam & bam conversions. Contribute to DarwinAwardWinner/mergesam development by creating an account on GitHub.
You can override this behaviour with the use of the `--save_align_intermeds` flag in which case it will contain the coordinate sorted alignment files in [`*.bam`](https://samtools.github.io/hts-specs/SAMv1.pdf) format. * `bwa/library/samtools_stats/` SAMtools `*.flagstat`, `*....