Sam/Bam Manipulation

Function: This tool generates a bigWig or bedGraph file of fragment or read coverages.
Usage: bamCoverage [options] -b reads.bam -o
Supported input format: BAM
Function: bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.
Usage: bamToBed [OPTIONS] -i <BAM>
Function: “guess” how RNA-seq sequencing were configured, particulary how reads were stranded for strand-specific RNA-seq data
Usage: -r gene_annotation.bed -i input.bam [options]
java -jar picard.jar
Function: Validates a SAM or BAM file.
Usage: java -jar picard.jar ValidateSamFile I=input.bam MODE=SUMMARY
samtools merge
Function: Merge multiple sorted alignment files, producing a single sorted output file that contains all the input records and maintains the existing sort order.
Usage: samtools merge [options] out.bam in1.bam ... inN.bam
Supported input format: BAM
Function: Convert BAM file into wig/bigWig format.
Usage: -s chrom.sizes -i sample.bam -o out [options]
bedtools bamtofastq
Function: Extract FASTQ records from sequence alignments in BAM format.
Usage: bedtools bamtofastq [OPTIONS] -i <BAM> -fq <FASTQ>
Supported input format: BAM
samtools view
Function: View, convert format, or filter (with different criteria) alignments.
Usage: samtools view [options] in.sam|in.bam|in.cram [region...]
Supported input format: BAM, CRAM, SAM
bedtools bamtobed
Function: Convert sequence alignments in BAM format into BED, BED12, and/or BEDPE records
Usage: bedtools bamtobed [OPTIONS] -i <BAM>
Supported input format: BAM
samtools stats
Function: samtools stats collects statistics from BAM files and outputs in a text format. The output can be visualized graphically using plot-bamstats.
Usage: samtools stats [options] in.sam|in.bam|in.cram [region...]
Supported input format: BAM, CRAM, SAM
java -jar picard.jar
Function: Applies one or more hard filters to a VCF file to filter out genotypes and variants.
Usage: java -jar picard.jar FilterVcf
samtools sort
Function: Converts SAM dataset into its binary, BAM.
Usage: samtools sort -O bam -o sorted_input.bam [INPUT SAM]
java -jar picard.jar
Function: Provides a large, configurable, FIFO buffer that can be used to buffer input and output streams between programs with a buffer size that is larger than that offered by native unix FIFOs (usually 64k).
Usage: java -jar picard.jar FifoBuffer
Function: The command bamtools split splits BAM file on user-specified property and creates a new BAM output file for each value found. In the given example, an output file input_alignments.MAPPED.bam is produced after -mapped split option is specified. Beside mapped, the split option can be: -paired, -reference, or -tag <tag_name>.
Usage: bamtools split -in input_alignments.bam -mapped
java -jar picard.jar
Function: Finds mendelian violations of all types within a VCF. Takes in VCF or BCF and a pedigree file and looks for high confidence calls where the genotype of the offspring is incompatible with the genotypes of the parents. Assumes the existence of format fields AD, DP, GT, GQ, and PL fields. Take note that the implementation assumes that reads from the PAR will be mapped to the female chromosomerather than the male. This requires that the PAR in the male chromosome be masked so that the aligner has a single coting to map to. This is normally done for the public releases of the human reference. Usage example: java -jar picard.jar FindMendelianViolations I=input.vcf \ TRIO=family.ped \ OUTPUT=mendelian.txt \ MIN_DP=20
Usage: java -jar picard.jar FindMendelianViolations