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| *[[QPLOT]] - Calculate & plot summary statistics | | *[[QPLOT]] - Calculate & plot summary statistics |
| *[[BamUtil: validate|Validate]] – Check file format & print statistics | | *[[BamUtil: validate|Validate]] – Check file format & print statistics |
| + | *[[VerifyBamID]] – Check sample identities for contamination/sample swap |
| + | **Genotype concordance based detection |
| + | **Estimate based on population allele frequencies without genotype data |
| + | *[[BamUtil: diff|Diff]] - Print the diffs between 2 bams |
| + | *[[BamUtil: stats|Stats]] - Print the diffs between 2 bams |
| + | |
| + | |
| + | ==== Rewrite SAM/BAM file ==== |
| *[[BamUtil: convert|Convert]] – Convert between SAM & BAM | | *[[BamUtil: convert|Convert]] – Convert between SAM & BAM |
− | *[[BamUtil: writeRegion|WriteRegion]] – Write only reads in the specified region | + | *[[SplitBam]] – Split into 1 file per Read Group |
| + | *[[BamUtil: splitChromosome|SplitChromosome]] – Split into 1 file per Chromosome |
| + | *[[BamUtil: writeRegion|WriteRegion]] – Write only reads in the specified region and/or have the specified read name |
| *[[Pileup]] – Pileup every base or just bases in specified region and write VCF | | *[[Pileup]] – Pileup every base or just bases in specified region and write VCF |
| *[[BamUtil: readIndexedBam|ReadIndexedBam]] - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file | | *[[BamUtil: readIndexedBam|ReadIndexedBam]] - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file |
− | *[[VerifyBamID]] – Check sample identities for contamination/sample swap
| |
− | **Genotype concordance based detection
| |
− | **Estimate based on population allele frequencies without genotype data
| |
| | | |
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| *[[TrimBam]] – Trim end of reads, changing read ends to ‘N’ & quality to ‘!’ | | *[[TrimBam]] – Trim end of reads, changing read ends to ‘N’ & quality to ‘!’ |
| *[[BamUtil: filter|Filter]] – Soft clip ends with too high mismatch % and mark unmapped if quality of mismatches is too high | | *[[BamUtil: filter|Filter]] – Soft clip ends with too high mismatch % and mark unmapped if quality of mismatches is too high |
− | | + | *[[BamUtil: revert|Revert]] - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags |
− | ==== Split the File ====
| + | *[[BamUtil: squeeze|Squeeze]] - Reduce files size by dropping OQ fields, duplicates, specified tags, using '=' when a base matches the reference, binning quality scores, and replacing readNames with unique integers |
− | *[[SplitBam]] – Split into 1 file per Read Group | |
− | *[[BamUtil: splitChromosome|SplitChromosome]] – Split into 1 file per Chromosome | |
− | | |
| | | |
| ==== Helper Tools to Print Readable Information ==== | | ==== Helper Tools to Print Readable Information ==== |