Inputs for hichipper

Based on the original design of hichipper users needed to specify the full HiC-Pro output. However, in subsequent versions, different inputs are accepted; specifically, only a valid fragments file.

While .bam files processed via different software (e.g. HiCUP) are not explicitly supported, one can easily convert .bam file formats into valid fragment pairs files using a combination of samtools and bedtools commands, such as this shown below:

samtools sort -n HiCUP_chr22.bam  | bamToBed -i - -bedpe |
	awk 'OFS="\t" {print $7,$1,int(($2+$3)/2), $9, $4, int(($5+$6)/2), $10}' > sample_converted.allValidPairs

The resulting sample_converted.allValidPairs file can be used as input to hichipper, using the --input-vi flag.