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Updates
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v.0.189
Now Meerkat works for BWA mem aligned genomes.
Fixed a bug in meerkat2vcf.pl, del and tandem_dup have incorrect orientations
in the old version.
Modified somatic_sv.pl and discon.pl to improve performance and removed -w
option in both.
v.0.188
Allow longer rg string.
Fixed a bug in somatic_sv.pl that would give del event type for del_ins and
call mechanism wrong for these cases
Meerkat works for whole exome sequencing data. Added filter_fusions.pl for WES
SV calls.
v.0.187
Improved bamreader (used in pre_process.pl) to reduce memory usage by 70%,
results are exactly the same as previous versions.
Allow character "'" in rg name.
v.0.186
Developed a tool discon.pl to provide number of discordant and concordant read
pairs across a breakpoint, such info can be used to calculate allele frequency.
Modified somatic_sv.pl to filter by allele frequency.
Fixed a bug in somatic_sv.pl to call unmapped reads as discordant pairs in some
rare cases.
Fixed a bug in fusions.pl to give negative value for homology in del_ins.
v.0.185
Developed a tool primers.pl to design PCR primers for validation.
Fixed a bug in fusions.pl that breakpoints in inssu events are flipped.
Improved somatic_sv.pl for 6-8x coverage genomes.
v.0.184
Improved somatic_sv.pl to handle long tail of insert size distribution
properly.
v.0.183
Removed dependency of PERL package biosamtools.
Fixed a bug in meerkat.pl that supporting split reads for deletions were
counted twice in previous versions.
Fixed a bug in somatic_sv.pl that some SVs are not properly filtered.
Updated fusions.pl to improve the fusion annotation, provide 5' and 3' fusion
partners.
v.0.182
Modified meerkat.pl to count realigned read pairs only once if they come from
the same read pair. It will give different number of supporting discordant read
pairs than previous versions. In previous versions, an unmapped read will be
cut into two parts and paired with the mapped mate to align to the reference
genome. Occasionally, both pairs will be discordant and counted twice. See step
1 and 2 of the Meerkat workflow figure at
http://compbio.med.harvard.edu/Meerkat/.
Fixed a bug in fusions.pl not outputing homology for inversions.
v.0.181
Fixed a bug in pre_process.pl for calling samtools.
v.0.180
Fixed a bug in meerkat.pl with scluster error.
v.0.179
Fixed a bug in filtering SVs in simple repeats and satellite repeats.
v.0.178
Removed dependency of mkfifo.
v.0.177
Added an option G to specify minimum mapping quality for reads to be used.
v.0.176
Two useful scripts provided: meerkat2vcf.pl to convert Meerkat output to VCF
format and fusions.pl to annotate fusion events into a uniformed format.