fun_setting

This function attempts to find the mutated bases in each read.

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_setting function

<dl><dt>pre</dt>
<dd>The 5' side bases of the sequence for searching.</dd>
<dt>post</dt>
<dd>The 3' side bases of the sequence for searching.</dd>
<dt>neighbor_seq</dt>
<dd>Short reference sequence around the mutation.</dd>
<dt>neighbor_length</dt>
<dd>The length from the mutation to the ends of the short
reference sequence.</dd>
<dt>alt_length</dt>
<dd>The length of altered bases.</dd></dl>

Arguments

Mutated position search function. — fun_setting

<dl>

<dt>pre</dt>
<dd>The 5' side bases of the sequence for searching.</dd>


<dt>post</dt>
<dd>The 3' side bases of the sequence for searching.</dd>


<dt>neighbor_seq</dt>
<dd>Short reference sequence around the mutation.</dd>


<dt>neighbor_length</dt>
<dd>The length from the mutation to the ends of the short
reference sequence.</dd>


<dt>alt_length</dt>
<dd>The length of altered bases.</dd>

</dl>

fun_setting: Mutated position search function.

Description

Usage

Value

Arguments