26 tool(s) found

Tool Description Topics Available version(s)
BedCov calculate read depth for a set of genomic intervals 5
Call and phase heterozygous SNPs 4
Filter SAM or BAM files on FLAG MAPQ RG LN or by region Filtering Nucleic acid sequence analysis 2
IdxStats reports stats of the BAM index file 8
Reheader copy SAM/BAM header between datasets 4
RmDup remove PCR duplicates 5
Samtools ampliconclip clip primer bases from bam files 2
samtools BAM to CRAM convert BAM alignments to CRAM format 4
Samtools calmd recalculate MD/NM tags 4
Samtools Chromosome Sizes order of storing aligned sequences 1
Samtools coverage computes the depth at each position or region 2
samtools CRAM to BAM convert CRAM alignments to BAM format 1
Samtools depth compute the depth at each position or region 4
Samtools fastx extract FASTA or FASTQ from alignment files 3
Samtools fixmate fill mate coordinates, ISIZE and mate related flags 3
Samtools flag_filter Use Samtools' view tool to filter alignments based on the flag field. 1
Samtools flagstat tabulate descriptive stats for BAM datset 8
Samtools markdup marks duplicate alignments 7
Samtools merge merge multiple sorted alignment files 3
samtools mpileup multi-way pileup of variants 11
Samtools sort order of storing aligned sequences 7
Samtools split BAM dataset on readgroups 5
Samtools stats generate statistics for BAM dataset 7
Samtools view - reformat, filter, or subsample SAM, BAM or CRAM 9
Slice BAM by genomic regions 5
vcfutils Program from SAMtools/BCFtools package (only vcf2fq command is implemented) 1