samtools merge tmp1.bam tmp2.bam 6. mpileup samtools mpileup [-EBugp] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam [...]] 从官方说明:Generate VCF, BCF or pileup for one or multiple BAM files可看出,可以用来和bcftools搭配Call...
samtools mpileup [-EBugp] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam [...]] 从官方说明:Generate VCF, BCF or pileup for one or multiple BAM files可看出,可以用来和bcftools搭配Call SNPs 最常用的几个参数: >-f The faidx-index...
#第一步:把sam文件转换成bam文件,我们得到map.bam文件 system"samtools view -bS map.sam > map.bam"; #第二步:sort 一下 BAM 文件,得到map.sorted.bam system"samtools sort map.b/am map.sorted"; #第三步:创建一个关于bam的索引文件,我们得到一个map.sorted.bam.bai的文件 system"samtools index map...
Example:samtools cat -o out.bam in1.bam in2.bam merge-- merge sorted alignments 将多个已经sort的bam文件进行合并 $ samtools merge Usage: samtools merge [-nurlf] [-h inh.sam] [-b <bamlist.fofn>] <out.bam> <in1.bam> [<in2.bam> ... <inN.bam>] Options: -n Input files are ...
sort sort alignment file split splits a file by read group quickcheck quickly check if SAM/BAM/CRAM file appears intact fastq converts a BAM to a FASTQ fasta converts a BAM to a FASTA collate $samtools collate Usage: samtools collate [-Ou] [-o <name>] [-n nFiles] [-l cLevel] <...
Work with bioinformatic files using Arrow, Polars, and/or DuckDB pythonbioinformaticsbiologyarrowbiopythonsamtoolspyarrowrust-bioduckdbpolars UpdatedNov 8, 2024 Rust divonlan/genozip Star159 A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to...
C 2 2 1 0 Updated Sep 22, 2023 klib Public Forked from attractivechaos/klib A standalone and lightweight C library C 0 MIT 621 0 0 Updated Jan 17, 2023 View all repositories People Top languages C Java Perl CSS HTML Most used topics bam cram ngs sam vcf Footer...
$ sambamba sort-t24gatk_markduplicates.bam-o gatk_markduplicates_sorted.bam $ sambamba index gatk_markduplicates_sorted.bam sambamba毕竟不如samtools常用,于是写了一个samtools版本。 代码语言:javascript 复制 $ samtools sort-@24-n tumor.bam-o query_sorted.bam ...
Allows users to interact with high-throughput sequencing data. SAMtools permits the manipulation of alignments in the SAM/BAM/CRAM formats: reading, writing, editing, indexing, viewing and converting SAM/BAM/CRAM format. It limits the mapping quality of
[bam_rmdup_core] 2 / 12 = 0.1667 in library 双端测序数据用samtools rmdup效果很差,很多人建议用picard工具的MarkDuplicates 功能 samtools 去除PCR冗余 ref:samtools 使用说明 samtools markdup [-llength] [-r] [-s] [-T] [-S]in.algsort.bam out.bam ...