Man pages for steverozen/DBSverify
Analyze Next Generation Sequencing Data to Verify Somatic Double-BaseSubstituion (DBS) Calls
| CategorizeReads | Categorizes the reads in one sam file. |
| CreateBAMSliceFileSamtools | Create a BAM slice as a SAM file using the samtools... |
| DBSConclusion | Examines every row of of DBS VCF already processed by... |
| DBS_conclusion_1_row | Examine 1 row of a DBS-only VCF that was already processed by... |
| GetAllBAMSlicesSamtools | Get and save all slices of BAM as specified by positions in a... |
| PCAWG_prep_BAM_list_and_BEDs | Specialized function for processing PCAWG Collaboratory BAMS. |
| PCAWG_read_table_and_evaluate_DBS | Read a table that specifies how to process VCFs and mini-BAMS... |
| Read_DBS_VCF_and_BAMs_to_verify_DBSs | Determine whether sequencing reads in fact support... |
| ReadSamfile | Read a "SAM file", discarding some reads that cannot be... |
| Read_SBS_VCF_and_BAMs_to_verify_DBSs | Aggressively merge SBSs into DBSs then determine whether... |
| RegressSAMDirectory | Compare the contents of two directories of .sam files |
| Slice2ReadSupport | Calculate the support for a putative DBS from the SAM slice... |
| VerifyDBSVcf | Given a VCF and the locations of a tumor and normal BAM files... |
