Sam/Bam Manipulation

bamCoverage
Function: This tool generates a bigWig or bedGraph file of fragment or read coverages.
Usage: bamCoverage [options] -b reads.bam -o coverage.bw
Supported input format: BAM
bamToBed
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>
java -jar picard.jar
Function: Validates a SAM or BAM file.
Usage: java -jar picard.jar ValidateSamFile I=input.bam MODE=SUMMARY
infer_experiment.py
Function: “guess” how RNA-seq sequencing were configured, particulary how reads were stranded for strand-specific RNA-seq data
Usage: infer_experiment.py -r gene_annotation.bed -i input.bam [options]
bam2wig.py
Function: Convert BAM file into wig/bigWig format.
Usage: bam2wig.py -s chrom.sizes -i sample.bam -o out [options]
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
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 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
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
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
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: 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
java -jar picard.jar
Function: Subset read data from a SAM or BAM fileThis tool takes a SAM or BAM file and subsets it to a new file that either excludes or only includes either aligned or unaligned reads (set using FILTER), or specific reads based on a list of reads names supplied in the READ_LIST_FILE.
Usage: java -jar picard.jar FilterSamReads I=input.bam O=output.bam READ_LIST_FILE=read_names.txt FILTER=filter_value
java -jar picard.jar
Function: Converts a FASTQ file to an unaligned BAM or SAM file. This tool extracts read sequences and base qualities from the input FASTQ file and writes them out to a new file in unaligned BAM (uBAM) format. Read group information can be provided on the command line. Three versions of FASTQ quality scales are supported: FastqSanger, FastqSolexa and FastqIllumina (see http://maq.sourceforge.net/fastq.shtml for details). Input FASTQ files can be in GZip format (with .gz extension).
Usage: java -jar picard.jar FastqToSam F1=file_1.fastq O=fastq_to_bam.bam SM=for_tool_testing
java -jar picard.jar
Function: Collect multiple classes of metrics. This 'meta-metrics' tool runs one or more of the metrics collection modules at the same time to cut down on the time spent reading in data from input files. Available modules include CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, QualityScoreDistribution, MeanQualityByCycle, CollectBaseDistributionByCycle, CollectGcBiasMetrics, RnaSeqMetrics, CollectSequencingArtifactMetrics, and CollectQualityYieldMetrics. The tool produces outputs of '.pdf' and '.txt' files for each module, except for the CollectAlignmentSummaryMetrics module, which outputs only a '.txt' file. Output files are named by specifying a base name (without any file extensions).
Usage: java -jar picard.jar CollectMultipleMetrics I=input.bam O=multiple_metrics R=reference_sequence.fasta