CURRENT WORK, DELETION READ CHECK:

Within the md_snv_position.R file, there are some changes being made concerning
how reads with deletions are being parsed for other mutations. No commits have
been made concerning this, but Chrissy will be working on them during the
beginning of 2017.

NEXT STEP, INSERTION READ CHECK:

Currently, any hard clip read overlapping a mutated location which contains an
insertion will be automatically marked as mutated at that location, unless the
read is otherwise unmutated. However, if there is a mutation which occurs on
that read, regardless of the position of the read’s mutation (if it is at the
same position as the recorded mutation or not) the read will be added to the
ovarall count of hard clipped reads with a mutation there.

It is this way currently because to implement a check for insertion mutations,
it requires more information than just looking at the CIGAR string and MD tag
from the BAM file. The SEQ value would also not give any insight into the
position of the insertion, so more investigation would have to be completed
before implementing this check.

This would all be done within the md_snv_position.R file, as a new case if
the read contains any insertins (indicated by an I in the CIGAR string).

I believe this check is very important though, and should be implemented as
soon as possible. This case of false positive hard clipped mutations within
reads with insertions is common, and is the pretext for many false positives
in initial analysis (dream challenge truth set).

NEXT STEP, QUALITY FILTER:

Currently, a read will be marked as having a mutation at a certain location
regardless of the quality of the read. This means that the reads which have
a very low mapping quality will also contribute to whether or not a mutation
is flagged as being a potential clipped artefact. To remedy this, a couple of
things could be taken into considerations when flagging a read as having a
clipped mutation.

	1) Mapping quality (mapq) of the read:
		A read as a whole is given a map quality, signified by the
		mapq attribute within the corresponding BAM file. The higher
		the mapping quality, the better the read. This mapping quality
		may be affected if the read is clipped.

	2) Base quality (qual) of each base within the read:
		Each base within the read has a corresponding quality associated
		with it, signified by the qual attribute in the corresponding
		BAM file. This attribute assigns an ASCII character to each base
		representing that base’s quality (bases themselves are kept in
		the seq attribute). Read the FASTQ link below for more information.

My suggestion is to implement a threshold (numerical or having some more
requirements)  as a cutoff for whether a clipped read should have its mutation
counted toward the total clipped mutation count at that location, based on both
mapping and base quality.


REFERENCES:

General BAM file formatting: https://samtools.github.io/hts-specs/SAMv1.pdf
FASTQ and base quality: https://en.wikipedia.org/wiki/FASTQ_format
MuTect quality overview: http://gatkforums.broadinstitute.org/gatk/discussion/4464/how-mutect-filters-candidate-mutations

AUTHOR:

L Christine Schreiner <christine.schreiner@sickkids.ca>

LAST UPDATED:

21-12-2016