Nextflow Modules
Showing module(s) with keyword "picard"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/gatk4/addorreplacereadgroups | Process | add replace read-group picard gatk | Assigns all the reads in a file to a single new read-group |
| nf-core/picard/addorreplacereadgroups | Process | add replace read-group picard | Assigns all the reads in a file to a single new read-group |
| nf-core/picard/bedtointervallist | Process | bed interval list picard convert | Creates an interval list from a bed file and a reference dict |
| nf-core/picard/cleansam | Process | clean bam picard sam clipping | Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads |
| nf-core/picard/createsequencedictionary | Process | sequence dictionary picard | Creates a sequence dictionary for a reference sequence. |
| nf-core/picard/extractfingerprint | Process | picard extract fingerprint bam | Computes/Extracts the fingerprint genotype likelihoods from the supplied file. It is given as a list of PLs at the fingerprinting sites. |
| nf-core/picard/filtersamreads | Process | bam filter picard sam | Filters SAM/BAM files to include/exclude either aligned/unaligned reads or based on a read list |
| nf-core/picard/fixmateinformation | Process | mate-pair picard bam sam | Verify mate-pair information between mates and fix if needed |
| nf-core/picard/liftovervcf | Process | vcf picard liftovervcf | Lifts over a VCF file from one reference build to another. |
| nf-core/picard/renamesampleinvcf | Process | picard picard/renamesampleinvcf vcf | changes name of sample in the vcf file |
| nf-core/picard/sortsam | Process | sort bam sam picard | Sorts BAM/SAM files based on a variety of picard specific criteria |