gatk过滤_gatk过滤标准

1

、

Determine parameters for filtering variation

SNPs

matching

any

of

these

conditions

will

be

considered

bad

and

filtered

out, i.e. marked FILTER in

the

output

VCF

file.

The

program

will

specify

which

parameter

was

chiefly

responsible

for

the exclusion of the SNP using the culprit annotation. SNPs that do

not

match

any

of

these

conditions

will

be

considered

good

and

marked PASS in the output VCF file.

QualByDepth (QD) 2.0

This

is

the

variant

confidence

(from

the QUAL field)

divided

by

the unfiltered depth of non-reference samples.

FisherStrand (FS) 60.0

Phred-scaled

p-

value

using

Fisher’s

Exact

Test

to

detect

strand

bias

(the

variation

being

seen

on

only

the

forward

or

only

the

reverse strand) in the reads. More bias is indicative of false positive

calls.

RMSMappingQuality (MQ) 40.0

This

is

the

Root

Mean

Square

of

the

mapping

quality

of

the

reads across all samples.

MappingQualityRankSumTest (MQRankSum) 12.5

This

is

the

u-based

z-approximation

from

the

Mann-Whitney

Rank Sum Test for mapping qualities (reads with ref bases vs. those

with the alternate allele). Note that the mapping quality rank sum