h5ngsqc is a Java program that allows to store NGS data in HDF5 files for being used on the QC Genomics platform. Stored data are fixed-size windows or bins:
- wiggles: number of reads overlapping a 50bp (default) bin
- localQCs: 500bp bins retained by NGS-QC Generator because they present a robust signal
java -jar h5ngsqc.jar BED TABLE CHROMSIZES OUTPUT [options]
BED is an alignment file in the BED format. Each line corresponds to a mapped read. The file can be gzip-compressed.
TABLE is a file generated by NGS-QC Generator. Can be gzip-compressed.
CHROMSIZES is an UCSC-like chromosome sizes file. Each line contains the name and the size of a chromosome.
OUTPUT is the output HDF5 file. If it already exists, it will be overwritten.
| Option | Description | Default |
|---|---|---|
| -s, --span INT | resolution in bp of wiggle bins | 50 |
| -e, --ext INT | read extension in bp for wiggle bins | 150 |
| --bg INT | background threshold for localQCs | 0 |
| -5 | enable 5-replicates localQCs | false |
| --skip | do not stop the program if a localQC or a read is on an unknown chromosome | false |
| --forgive | skip invalid lines instead of stopping the program | false |
| --quiet | do not display progress messages | false |
While computing wiggles, two values are associated at each bin: the intensity, and the intensity without PCR duplicates. To identify PCR duplicates, the BED file has to be sorted as follows:
sort -k1,1V -k2,2n profile.bed > profile.sort.bed
- gzip-compressed files support
- read BED from stdin