samtools sort test.bam -o test_sorted Creating a BAM index file samtools index test_sorted.bam test_sorted.bai Converting a BAM file to a SAM file Note: remember to use -h to ensure the converted SAM file contains the header information. Generally, I suggest storing only sorted BAM files ...
khash_str2str.h reheader: support spaces in sample names Jan 14, 2016 kheap.h New sort command Jul 7, 2017 kmin.c call: Original bcftools' -c calling now functional Oct 1, 2013 kmin.h call: Original bcftools' -c calling now functional Oct 1, 2013 main.c Happy New Year Jan 18,...
Loading Type Language Sort Showing 10 of 15 repositories htslib Public C library for high-throughput sequencing data formats C 817 443 142 25 Updated Jan 8, 2025 bcftools Public This is the official development repository for BCFtools. See installation instructions and other documentation her...
example_intervals.list improper_pairs_1.fq parquet_lister_dir_empty small_missing.vcf unordered.sam fastq_noqual.fq improper_pairs_2.fq proper_pairs_1.fq small_realignment_targets.intervals unsorted.sam hadoop@Mcnode1:~/cloud/adam/xubo/data/data_HDFS/adam/resources$ samtools sort -o smallSort....
-H, --no-header do not print @HDline -o, --output FILE file to write out dict file [stdout] -s, --species STR species -u, --uri STR URI [file:///abs/path/to/file.fa] 对基因组文件建立一个序列字典文件 $samtools dict -o hg19.dict hg19.fa ...
samtools sort [-l level] [-m maxMem] [-o out.bam] [-O format] [-n] [-T tmpprefix] [-@ threads] [in.sam|in.bam|in.cram] Sort alignments by leftmost coordinates, or by read name when -n is used. An appropriate @HD-SO sort order header tag will be added or an existing on...
使用bwa,hisat2等比对软件,常会得到sam文件,此文是对多个sam转化/排序/建立index的命令 vim sam2bam.sh#按一下i进入编辑模式,写入以下内容!/bin/bashforiinY51015cold-1Y51015cold-2#sam文件的名字dosamtools view-@30-bS ${i}.sam|samtools sort-@30-o ${i}.sort.bam $#转化并排序done ...
samtools view -S test.sam -b > test.bam #比对到负链的reads samtools view -f 16 test.bam # 比对到参考基因组的序列,flag值为4代表比对不上 samtools view -F 4 test.bam bam排序和建索引 -@, --threads 可以添加线程数 samtools sort test.bam -o test_sort.bam ...
samtools sorttmp1.bam tmp1.sorted samtoolsindex tmp1.sorted.bam samtools mpileup -d 1000 -gSDf ../../../ref-database/hg19.fa tmp1.sorted.bam |bcftools view -cvNg – >tmp1.vcf 因为这个软件都是与bwa和bowtie等能产生sam文件的软件合作才能使用。
private static SAMSequenceRecord readSequenceRecord(final BinaryCodec stream, final String source) { final int nameLength = stream.readInt(); if (nameLength <= 1) { throw new SAMFormatException("Invalid BAM file header: missing sequence name in file " + source); } final String sequenceName...