bti is a small tool to quickly retrieve alignments in a bam file by tag and is a minor modification and fork of the bri repo. With 10x genomics and other single cell data, it is sometimes desirable to extract all of the alignments for a particular cell or molecular barcode. bti is designed for this usecase and provides both a command line interface and htslib-inspired API. The index for 15Gb of 10x Genomics single cell RNA-Seq data with 400K barcodes is under 20 MB, and querying takes ~ 1 sec per cellbarcode.
git clone https://github.com/kriemo/bti.git
cd bti
make HTSDIR=/path/to/htslib
First sort the bam file by the tag of interest (only string type "Z" tags are implemented) using samtools sort -t CB
Then index the bam file by tag :
> bti index CB test/cb_tag_sorted_small.bam
Extract the alignments for a particular tag value (output is in BAM):
> bti get test/cb_tag_sorted_small.bam AAACCTGGTACGCTGC-1 | samtools view | head -n 2
K00282:115:HJTMNBBXX:5:1223:0:2858381 0 1 88217701 255 98M * 0 0AATGACATCCATGCTCGATCACAACCTGCTCTCAAAGTGACACGTTCCAGCTCTGGGGACAAAGGCCGCCATCTCTCTCAATGGCTTCTCACCTCCCA AAFAFJJJJJJJJJJFAJJJFFAAJFJFJJJJJ<7AAFJJJFFJAFJA<-FJJFJJFF-A<-<AFJFFJFAAAFJJFJJFAJJFJJJJJJ7FFJJJJF NH:i:1 HI:i:1 AS:i:94 nM:i:1 NM:i:1 CR:Z:AAACCTGGTACGCTGC CY:Z:AAFFFJJJJJJJJJJJ CB:Z:AAACCTGGTACGCTGC-1 UR:Z:AAAGCACAGA UY:Z:JJJJJJJJJJ UB:Z:AAAGCACAGA BC:Z:GAAGGCTG QT:Z:AAFFF-AJ
K00282:115:HJTMNBBXX:5:2108:0:3201626 0 1 165292120 255 27S71M * 0 0AAGCAGTGGTATCAACGCAGAGTACATGGGCGCCTTTAATCCCAGCACTCGGGAGGCAGAGGCAGGCGGATTTCTGAGTTAGAGGCCAGCCTGGTCTA AA<AFFJFFJ7FJFJJJJJJAAJAJ7FJJJJJF77FF7<<<-7<7-77<7FJJ7JJ<7F7AJF-AFAJJ77AF7AJ-7FF7F7AJ7A7A7FFJJAAAA NH:i:1 HI:i:1 AS:i:69 nM:i:0 NM:i:0 CR:Z:AAACCTGGTACGCTGC CY:Z:AAFF-FFJJJFJFJJA CB:Z:AAACCTGGTACGCTGC-1 UR:Z:TCTTGAGGGG UY:Z:JFJJJFJJJJ UB:Z:TCTTGAGGGG BC:Z:TGGATTGC QT:Z:AAFAFJJA