19 tool(s) found

Tool Description Topics Available version(s)
BAM coverage statistics using samtools idxstats and depth 1
Batch-get-subseq Batch extract sub-sequences from new draft rice genomes 1
BedCov calculate read depth for a set of genomic intervals 3
Call and phase heterozygous SNPs 4
CalMD recalculate MD/NM tags 2
Filter SAM or BAM files on FLAG MAPQ RG LN or by region Filtering Nucleic acid sequence analysis 3
Flagstat tabulate descriptive stats for BAM datset 7
IdxStats tabulate mapping statistics for BAM dataset 8
MPileup call variants 10
Reheader copy SAM/BAM header between datasets 2
RmDup remove PCR duplicates 7
Samtools extract FASTA or FASTQ from a SAM file 1
Samtools fixmate fill mate coordinates, ISIZE and mate related flags 1
Samtools parallel mpileup Samtools mpileup (supporting parallelization) 2
Slice BAM by genomic regions 6
Sort BAM dataset 7
Split BAM dataset on readgroups 2
Stats generate statistics for BAM dataset 4
vcfutils Program from SAMtools/BCFtools package (only vcf2fq command is implemented) 1