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Queries on bam file of single cell per genome position for finding rare mutations

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## Queries on bam file of single cell per genome position for finding rare mutations

single-cell-bam-queries.py –help

usage: single-cell-bam-queries.py [-h] –input-file INPUT_FILE –output-file
OUTPUT_FILE [–coordinates COORDINATES] [–filtered-cell-barcodes-file FILTERED_CELL_BARCODES_FILE] [–min-mapq MIN_MAPQ] [–max-gene-length MAX_GENE_LENGTH] [–threads THREADS] [–min-cells MIN_CELLS] [–max-cells MAX_CELLS] [–min-mutated-umis MIN_MUTATED_UMIS] [–max-mutated-umis MAX_MUTATED_UMIS] [–min-reads-per-non-mutated-umi MIN_READS_PER_NON_MUTATED_UMI] [–max-reads-per-non-mutated-umi MAX_READS_PER_NON_MUTATED_UMI] [–min-non-mutated-umis MIN_NON_MUTATED_UMIS] [–max-non-mutated-umis MAX_NON_MUTATED_UMIS] [–min-reads-per-mutated-umi MIN_READS_PER_MUTATED_UMI] [–max-reads-per-mutated-umi MAX_READS_PER_MUTATED_UMI] [–enable-cells-with-invalid-umis-num] [–enable-umis-with-invalid-reads-num] [–tag-of-umi TAG_OF_UMI] [–tag-of-cell-barcode TAG_OF_CELL_BARCODE] [–umi-start UMI_START] [–umi-length UMI_LENGTH] [–cell-barcode-start CELL_BARCODE_START] [–cell-barcode-length CELL_BARCODE_LENGTH] [–log-file LOG_FILE]

Queries on bam file of single cell per genome position.

The bam file must be sorted and indexed with the commands:

samtools sort filename.bam > filename.sorted.bam samtools index filename.sorted.bam

By default the umi and barcode cells are comptible to bam files from cellranger. For other formats you need to change the parameters of tags and cell barcodes.

Pre-request: python package: pysam

optional arguments:
-h, --help show this help message and exit
--input-file INPUT_FILE
 Full path to input .bam or .sam file (default: None)
--output-file OUTPUT_FILE
 Full path to output file name (default: None)
--coordinates COORDINATES
 Coordinates of the genome. The default is all genome. For example: chr1:1000000-2000000, or for all chromosom: chr1 (default: all)
--filtered-cell-barcodes-file FILTERED_CELL_BARCODES_FILE
 Text file with list of cell barcodes. Counts only these cells (optional) (default: None)
--min-mapq MIN_MAPQ
 Minimum quality of the read mapping (default: 10)
--max-gene-length MAX_GENE_LENGTH
 Maximum length of the gene. Reads that will be mapped to longer bases will be discarded (default: 100000)
--threads THREADS
 number of threads. You can run the chromosome itself in several threads. You can use this prameter only if you specify the start and end coordinates explicitely in the format: chr1:0-14000000 or if the bam file contains header lines with the lengths of the chromosomes, you can check it with the commands: samtools view -h filename.bam (default: 1)
--min-cells MIN_CELLS
 mininum cells in genome position that contains the number of umis and reads according to the other parameters (default: 1)
--max-cells MAX_CELLS
 maximum cells in genome position that contains the number of umis and reads according to the other parameters (default: 1000000000)
--min-mutated-umis MIN_MUTATED_UMIS
 mininum umis per cell that all reads contain mutation in the position (default: 1)
--max-mutated-umis MAX_MUTATED_UMIS
 maximum umis per cell that all reads contain mutation in the position (default: 1000000000)
--min-reads-per-non-mutated-umi MIN_READS_PER_NON_MUTATED_UMI
 mininum reads in at least one of umis in the cell in genome position (default: 1)
--max-reads-per-non-mutated-umi MAX_READS_PER_NON_MUTATED_UMI
 maximum reads in at least one of umis in the cell in genome position (default: 1000000000)
--min-non-mutated-umis MIN_NON_MUTATED_UMIS
 mininum umis per cell that all reads not contain mutation in the genome position (default: 1)
--max-non-mutated-umis MAX_NON_MUTATED_UMIS
 maximum umis per cell that all reads not contain mutation in the genome position (default: 1000000000)
--min-reads-per-mutated-umi MIN_READS_PER_MUTATED_UMI
 mininum reads in at least one of umis in the cell in genome position (default: 1)
--max-reads-per-mutated-umi MAX_READS_PER_MUTATED_UMI
 maximum reads in at least one of umis in the cell in genome position (default: 1000000000)
--enable-cells-with-invalid-umis-num
 enable positions that contain cell/s with not valid umis number (according to ther range in the other parameters) (default: False)
--enable-umis-with-invalid-reads-num
 enable positions that contain umi/s with not valid reads number (according to ther range in the other parameters) (default: False)
--tag-of-umi TAG_OF_UMI
 the tag of umi in bam file (default: UR)
--tag-of-cell-barcode TAG_OF_CELL_BARCODE
 the tag of umi in bam file (default: CR)
--umi-start UMI_START
 location in tag where the umi start (0-based) (default: 0)
--umi-length UMI_LENGTH
 length of umi (default: 10)
--cell-barcode-start CELL_BARCODE_START
 location in tag where the cell barcode start (0-based) (default: 0)
--cell-barcode-length CELL_BARCODE_LENGTH
 length of cell barcode (default: 16)
--log-file LOG_FILE
 Log File (default: None)

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