fun_repeat_check

This function attempts to check the repetitive sequence around the mutation.

Clinical sequencing of tumor is usually performed on formalin-fixed
and paraffin-embedded samples and have many sequencing errors. We found that
the majority of these errors are detected in chimeric read caused by
single-strand DNA with micro-homology. Our filtering pipeline focuses on the
uneven distribution of the artifacts in each read and removes such errors in
formalin-fixed and paraffin-embedded samples without over-eliminating the
true mutations detected in fresh frozen samples.

Masachika Ikegami

MicroSEC

Sequence Error Filter for Formalin-Fixed and Paraffin-Embedded
Samples

fun_repeat_check function

<dl><dt>rep_a</dt>
<dd>The shorter sequence of Ref and Alt.</dd>
<dt>rep_b</dt>
<dd>The longer sequence of Ref and Alt.</dd>
<dt>ref_seq</dt>
<dd>Reference sequence around the mutation.</dd>
<dt>ref_width</dt>
<dd>Search length for ref_seq.</dd>
<dt>del</dt>
<dd>Insertion: 0, Deletion: 1</dd></dl>

Arguments

Repeat check function. — fun_repeat_check

<dl>

<dt>rep_a</dt>
<dd>The shorter sequence of Ref and Alt.</dd>


<dt>rep_b</dt>
<dd>The longer sequence of Ref and Alt.</dd>


<dt>ref_seq</dt>
<dd>Reference sequence around the mutation.</dd>


<dt>ref_width</dt>
<dd>Search length for ref_seq.</dd>


<dt>del</dt>
<dd>Insertion: 0, Deletion: 1</dd>

</dl>

fun_repeat_check: Repeat check function.

Description

Usage

Value

Arguments