Version 3.2 (#30)

- Filter reads on rq (>=0.99), if rq is present in input bam 
- Add a `targeted` option for targeted data to drop the assumption of uniform coverage across the genome 
- Add two optional parameters for targeted data: `min-read-variant` and `min-read-haplotype`
- Update coordinates of some target regions to include full genes whenever possible
- Add TNXB as a region on its own so that the full gene can be genotyped
- Improve fusion calling in cases of homozygous deletion 
- Add some homozygous sites to cover target regions evenly during phasing to improve read assignment to haplotypes and variant calling
- Update a few gene-specific callers: hba, smn1, ikbkg, ncf1, rccx and pms2
- Support cram as input 
- Standardize haplotype naming across regions

Author: xiao-chen-xc

README.md

@@ -86,6 +86,10 @@ Optional parameters:
 - `--genome`: Genome reference build. Default is `38`. If `37` or `19` is specified, Paraphase will run the analysis for GRCh37 or hg19, respectively (note that only 11 medically relevant [regions](docs/regions.md) are supported now for GRCh37/hg19).
 - `--gene1only`: If specified, variants calls will be made against the main gene only for SMN1, PMS2, STRC, NCF1 and IKBKG, see more information [here](docs/vcf.md).
 - `--novcf`: If specified, no VCF files will be produced.
+- `--write-nocalls-in-vcf`: If specified, Paraphase will write no-call sites in the VCFs, marked with LowQual filter.
+- `--targeted`: If specified, paraphase will not assume depth is uniform across the genome. See more information on running targeted data [here](docs/targeted_data.md).
+- `--min-read-variant`: Partially controls the number of supporting reads for a variant to be used for phasing. The cutoff for variant-supporting reads is determined by min(this number, max(5, depth\*0.11)). Default is 20 (at standard WGS depth, it is overwritten by max(5, depth*0.11)).
+- `--min-read-haplotype`: Minimum number of unique supporting reads for a haplotype. Default is 4.
 - `--samtools`: path to samtools. If the paths to samtools or minimap2 are not already in the PATH environment variable, they can be provided through the `--samtools` and `--minimap2` parameters.
 - `--minimap2`: path to minimap2
 

docs/targeted_data.md

@@ -0,0 +1,14 @@
+# Running Paraphase on targeted data
+
+Paraphase can work with targeted data, such as:
+- Hybrid capture based enrichment data
+- CRISPR-Cas9 targeted data
+- Amplicon data
+
+The config file may need to be modified based on the design of the target panel. Please reach out to Xiao Chen (xchen@pacificbiosciences.com) if you need assistance.
+
+Paraphase provides a few options for users to better work with targeted data: 
+1) Use the `--targeted` option to drop the assumption of uniform coverage across the genome.
+2) Additionally there are two optional parameters one can tune for targeted data:
+- `--min-read-variant`: Partially controls the number of supporting reads for a variant for identifying variants used for phasing. The cutoff for variant-supporting reads is determined by min(this number, max(5, depth\*0.11)). Default is 20. At standard WGS depth, the default value is overwritten by max(5, depth*0.11). For targeted data with high coverage, set this number relatively high to avoid picking up sequencing errors and to reduce run time. For example, if you expect your per-haplotype depth is 200, you can set `--min-read-variant` to 40 or even higher.
+- `--min-read-haplotype`: Minimum number of unique supporting reads for a haplotype. Default is 4. For targeted data with high coverage, this cutoff can be increased to reduce errors and to reduce run time.

paraphase/__init__.py

@@ -1 +1 @@
-__version__ = "3.1.2"
+__version__ = "3.2.0"

paraphase/data/19/config.yaml

@@ -29,15 +29,15 @@ smn1:
 pms2: 
   genes: PMS2
   check_nm: 0.1
-  realign_region: chr7:6004631-6049631
-  extract_regions: chr7:6004631-6033041 chr7:6773174-6799427
+  use_r2k: True
+  realign_region: chr7:6004631-6049131
+  extract_regions: chr7:6004631-6049131 chr7:6773174-6799427
   gene2_region: chr7:6773174-6799427
-  right_boundary: 6033081
   pivot_site: 6026200
-  noisy_region: [[6020511, 6020611], [6019294, 6019300], [6015581, 6015711], [6028131, 6031981], [6032411, 6033031]]
+  noisy_region: [[6020511, 6020611], [6019294, 6019300], [6015581, 6015711], [6036207, 6036263], [6042921, 6042979], [6048361, 6048369]]
   is_reverse: True
   add_sites: ["6026200_G_A"]
-  clip_3p_positions: [6033041]
+  clip_3p_positions: [6028720]
 rccx: 
   genes: CYP21A2,C4A,C4B,TNXB
   is_tandem: True
@@ -95,15 +95,14 @@ cfc1:
 ikbkg: 
   genes: IKBKG
   use_supplementary: True
-  realign_region: chrX:153783815-153803263
-  extract_regions: chrX:153784098-153800231 chrX:153860696-153876829
+  realign_region: chrX:153775825-153800231
+  extract_regions: chrX:153775825-153800231 chrX:153860696-153876829
   gene2_region: chrX:153860252-153877274
   clip_3p_positions: [153797929]
-  clip_5p_positions: [153785351]
+  clip_5p_positions: [153783719, 153785351]
   add_sites: ["153784097_C_G", "153798031_T_G"]
   pivot_site: 153784097
-  left_boundary: 153783915
-  right_boundary: 153797929
+  right_boundary: 153798131
   deletion1_size: 11700
   deletion1_name: "153786229_del_11700"
   deletion1_in_gene1: "153786229_DEL_153797929"
@@ -112,8 +111,9 @@ ikbkg:
   del1_3p_pos2: 153786245
   del1_5p_pos1: 153797031
   del1_5p_pos2: 153797071
-  noisy_region: [[153795215, 153795402], [153784084, 153784091], [153793571, 153793618]]
+  noisy_region: [[153795215, 153795402], [153783765, 153783965], [153784084, 153784091], [153793571, 153793618]]
   is_reverse: True
+  check_nm: 0.08
 ncf1:
   genes: NCF1
   check_nm: 0.1
@@ -159,10 +159,11 @@ opn1lw:
   exon3_variants: [[["153418460_C_A"], "M", "L"], [["153418514_G_A", "153418516_G_T"], "I", "V"], [["153418524_C_T"], "V", "A"], [["153418535_A_G"], "V", "I"], [["153418541_T_G"], "A", "S"]]
 hba:
   genes: HBA1,HBA2
-  realign_region: chr16:221799-223899
+  realign_region: chr16:221799-225499
   extract_regions: chr16:218655-227540
-  clip_5p_positions: [221988]
-  clip_3p_positions: [223728]
+  check_nm: 0.25
+  clip_5p_positions: [221988, 222889]
+  clip_3p_positions: [223728, 225045]
   is_tandem: True
   depth_region: [[209999, 239999]]
   noisy_region: [[222416, 222417]]