📦 biobambam2

B

• bam12auxmerge(1)merge two BAM files✨
• bam12split(1)project rank pairs produced by bamcollate2 to single ranks per read✨
• bam12strip(1)remove rank left by bam12split from read names✨
• bamadapterclip(1)remove the adapters marked by bamadapterfind✨
• bamadapterfind(1)find adapter contamination in sequencing reads✨
• bamalignfrac(1)compute fraction of aligned bases in alignment file✨
• bamauxmerge(1)merge information in unmapped and mapped alignment files✨
• bamauxmerge2(1)merge information in unmapped and mapped BAM files✨
• bamauxsort(1)filter auxiliary tags from BAM file✨
• bambisect(1)find reduced size BAM file on which a program fails✨
• bamcat(1)concatenate BAM files✨
• bamchecksort(1)check sort order of a BAM file✨
• bamclipreinsert(1)reinsert query sequence fragments removed by bamadapterclip✨
• bamclipXT(1)reinsert query sequence fragments removed by bamadapterclip✨
• bamcollate2(1)collate reads in a SAM, BAM or CRAM file by name✨
• bamconsensus(1)compute rough consensus sequence from alignments✨
• bamdownsamplerandom(1)downsample a SAM, BAM or CRAM file✨
• bamfeaturecount(1)evaluate alignments produce by an RNA-seq aligner✨
• bamfillquery(1)fill query sequences into BAM files✨
• bamfilteraux(1)filter auxiliary tags from BAM file✨
• bamfilterflags(1)remove entries from BAM files matching a given set of flags✨
• bamfilterheader(1)filter auxiliary tags from BAM file✨
• bamfilterheader2(1)filter auxiliary tags from BAM file✨
• bamfiltermc(1)remove MC aux fields for reads with unmapped mates✨
• bamfilterrg(1)filter read groups from a BAM file✨
• bamfixmateinformation(1)fix mate pair information in BAM files✨
• bamflagsplit(1)sort BAM files by coordinate or query name✨
• bamindex(1)create index for BAM file✨
• bamintervalcomment(1)sort BAM files by coordinate or query name✨
• bammarkduplicates(1)mark duplicate reads/alignments in BAM files✨
• bammarkduplicates2(1)mark duplicate reads/alignments in BAM files✨
• bammarkduplicatesopt(1)mark duplicate reads/alignments in BAM files✨
• bammaskflags(1)remove flags from alignments✨
• bammdnm(1)compute MD and NM fields✨
• bammerge(1)merge BAM files✨
• bamrank(1)insert the rank (line number) of each alignment as an auxiliary field for tag zz✨
• bamranksort(1)sort BAM files by rank✨
• bamrecalculatecigar(1)concatenate BAM files✨
• bamrecompress(1)recompress BAM file✨
• bamreset(1)reset BAM file to unaligned state✨
• bamseqchksum(1)produce checksums for primary data in BAM files✨
• bamsormadup(1)sort name collated SAM or BAM file by coordinate and mark duplicates or sort SAM or BAM file by query name✨
• bamsort(1)sort BAM files by coordinate or query name✨
• bamsplit(1)split BAM files✨
• bamsplitdiv(1)split BAM file into a set of BAM files✨
• bamstreamingmarkduplicates(1)mark duplicate reads✨
• bamtagconversion(1)convert old tags to new ones✨
• bamtofastq(1)convert SAM, BAM or CRAM files to FastQ✨
• bamvalidate(1)validate BAM file✨
• bamzztoname(1)move the rank of an alignment stored as an auxiliary field to the alignments name✨

F

• fastaexplod(1)split multi sequence FastA file into one file per sequence✨
• fastqtobam(1)convert FastQ to unmapped BAM✨
• filtergtf(1)filter a gtf annotation file for use with bamfeaturecount✨

N

• normalisefasta(1)normalise line length in a FastA file✨