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GalaxyCat
v0.5.0
Tools
Topics
Instances
About
Examples :
samtools
,
bed
,
topic:conversion
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