Bam file to count table

Bam file to count table

Examples:

Amount of reads per sample --sampleTags SM per chromosome -joinedFeatureTags reference_name

bamToCountTable.py test.bam --sampleTags SM -joinedFeatureTags reference_name -o reads_per_sample.csv

Amount of molecules --dedup per sample --sampleTags SM per chromosome -joinedFeatureTags reference_name

bamToCountTable.py test.bam --sampleTags SM -joinedFeatureTags reference_name --dedup -o molecules_per_sample.csv

Bin molecules in 250kb bins -bin 250_000, where the bin is determined by the DS tag -binTag DS and counted molecule have at least 20 mapping quality -minMQ 20

bamToCountTable.py test.bam -joinedFeatureTags reference_name -minMQ 20 --dedup -binTag DS -bin 250_000 -o molecules_binned_250k.csv

Bin molecules in 250kb bins -bin 250_000 with a sliding window of 50kb -sliding 50_000 where the location is determined by the starting position of the read -binTag reference_start, ignore reads with alternative hits --filterXA and mapping quality below 60 -minMQ 60

bamToCountTable.py test.bam -joinedFeatureTags reference_name -minMQ 60 --filterXA --dedup -binTag reference_start -bin 250_000 -o molecules_binned_250k_sliding_50k.csv