Handle-umis - These tools are compatible with the pipeline SAIP using UMIs and smcounter2
This module has 4 packages :
- add_umi
*Add UMIs to the read_id.*
This is useful for the pipeline SAIP using UMIs after the read-trimming.
- add_tags
*Add primer and UMI tags to all reads.*
This is useful for the pipeline SAIP using UMIs after the clustering with umi_tools group.
- txt_to_fasta
*Convert the primer file into fasta.*
This is used with cutadapt for the gene specific primer clipping.
- txt_to_vcf
*Convert the variants file into vcf.*
This is used after smCounter2 before the annotations with SNPEff et SNPSift.