SvABA
r2c.db
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Quick queries
Top contigs by read count
contigs ordered by n_reads desc, top 200
PASS contigs only
requires postprocess to have run
PASS + somatic contigs
tumor-specific calls only
Top BPs by split-supporter count
groups bp_id (or comma-list) by row count
Reads supporting one BP
use the bp_id from bps.txt's col 52
All reads on one contig
svaba_grep_contig equivalent
Read support breakdown
split / disc / both / none
Per-contig support summary
n_split / n_disc rolled up per contig
Schema
contigs
cname
TEXT PK
contig_len
INT
seq
TEXT
frags
TEXT
bps
TEXT
n_reads
INT
reads
cname
TEXT FK
read_id
TEXT
chrom
TEXT
pos
INT
flag
INT
r2c_cigar
TEXT
r2c_start
INT
r2c_rc
INT
r2c_nm
INT
support
TEXT
split_bps
TEXT
disc_bps
TEXT
r2c_score
REAL
native_
REAL
seq
TEXT
pass_cnames
cname
TEXT PK
somatic
INT 0/1
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