scotch-data-grch37

GRCh37 region feature data for Scotch indel caller. (GRCh38 features available here.)

Data

1. chromosome
2. position
3. nistHC

• whether the position is in NIST-high-confidence regions
• ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv3.3.2/GRCh37/HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel.bed

4. repMasker

• whether the position is in RepeatMakser-masked regions
• UCSC Genome Browser Table Browser --> Genome: Human, Group: All Tables, Table: rmsk

5. segDups

• whether the position lies in segmental duplications
• ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/NA12878/analysis/NIST_union_callsets_06172013/superdupsmerged_all_sort.bed.gz

6. LCR

• whether the position lies in low-complexity regions
• hs37d5-LCRs.bed.gz, available at https://figshare.com/articles/Low_complexity_regions_in_hs37d5/969685

7. gc50

• GC content within a 50-bp window
• calculated with bedtools nuc

8. gc1000

• GC content within a 1000-bp window
• calculated with bedtools nuc

9. map100

• mappability score
• UCSC Genome Browser Table Browser --> Genome: Human, Group: All Tables, Table: wgEncodeCrgMapabilityAlign100mer

10. uniq35

• uniqueness score within 35 bp
• UCSC Genome Browser Table Browser --> Genome: Human, Group: All Tables, Table: wgEncodeDukeMapabilityUniqueness35bp