MACS3.Signal.PosReadsInfo module

All Parser classes

class MACS3.Signal.PosReadsInfo.PosReadsInfo

Bases: object

add_C(read_index, read_allele, read_bq, strand, Q=20)

add_T(read_index, read_allele, read_bq, strand, tip, Q=20)

Strand 0: plus, 1: minus

Q is the quality cutoff. By default, only consider Q20 or read_bq > 20.

apply_GQ_cutoff(min_homo_GQ=50, min_heter_GQ=100)

apply_deltaBIC_cutoff(min_delta_BIC=10.0)

call_GT(max_allowed_ar=0.99)

Require update_top_alleles being called.

filterflag()

raw_read_depth(opt='all')

toVariant()

to_vcf()

Output REF,ALT,QUAL,FILTER,INFO,FORMAT, SAMPLE columns.

top12alleles()

update_top_alleles(min_top12alleles_ratio=0.8, min_altallele_count=2, max_allowed_ar=0.95)

Identify top1 and top2 NT. the ratio of (top1+top2)/total