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Old 08-07-2018, 01:24 AM   #1
mhmtgenc
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Default How to get a report like stuff of a bam file how many percent of the exons are cover

Dear Collegues,

Lets say I have a miseq run and have the .bam file from the squencer and I would like to know how many percent of the exons (specific genes) are coverred in these .bam files?

Is it possible?

Thanks in advance
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Old 08-07-2018, 03:58 AM   #2
Gopo
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Try CollectHSmetrics - part of Picard Tools
For details see:
https://broadinstitute.github.io/pic...-overview.html
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Old 08-07-2018, 04:22 AM   #3
mhmtgenc
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Quote:
Originally Posted by Gopo View Post
Try CollectHSmetrics - part of Picard Tools
For details see:
https://broadinstitute.github.io/pic...-overview.html
So how coul I be able to get a BED file or prepare it by myself? Could you give me a clue or a tutorial of this. Cause I have trouble on this. I know this is hard to expalin it here but can I get any file or manual for this?
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Old 08-08-2018, 11:11 PM   #4
Gopo
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You will have to make the BED file yourself. Here is a guide:

Code:
# install picard
cd ~/bin/
wget https://github.com/broadinstitute/picard/releases/download/2.18.10/picard.jar
mv picard.jar picard-2.18.10.jar

# index reference (Reference is AmexG_v3.0.0.fa)
samtools faidx AmexG_v3.0.0.fa

# create sequence dictionary
java -Xmx64g -jar ~/bin/picard-2.18.10.jar CreateSequenceDictionary \
R=AmexG_v3.0.0.fa \
O=AmexG_v3.0.0.dict

# Convert BED to interval list
java -jar ~/bin/picard-2.18.10.jar BedToIntervalList \
I=rfs.immunome.bed \
O=rfs.immunome.interval.list \
SD=AmexG_v3.0.0.dict

# run CollectHsMetrics
java -Xmx64g -jar ~/bin/picard-2.18.10.jar CollectHsMetrics \
BAIT_INTERVALS=/ssdwork/jelber2/rfs/rfs.immunome.interval.list \
BAIT_SET_NAME=Immunome \
TARGET_INTERVALS=/ssdwork/jelber2/rfs/rfs.immunome.interval.list \
METRIC_ACCUMULATION_LEVEL=SAMPLE \
R=/ssdwork/jelber2/rfs/AmexG_v3.0.0.fa \
I=ALL-samples.bam \
O=ALL-samples-coverage-metrics.txt

# if needed, add readgroups
java -Xmx64g -jar ~/bin/picard.jar AddOrReplaceReadGroups \
I=ALL-samples.bam \
O=ALL-samples-RG.bam \
SORT_ORDER=coordinate \
RGPL=illumina \
RGPU=barcode \
RGLB=Lib1 \
RGID=all \
RGSM=all \
VALIDATION_STRINGENCY=LENIENT

# run CollectHsMetrics with ReadGroups added to BAM
java -Xmx64g -jar ~/bin/picard-2.18.10.jar CollectHsMetrics \
BAIT_INTERVALS=/ssdwork/jelber2/rfs/rfs.immunome.interval.list \
BAIT_SET_NAME=Immunome \
TARGET_INTERVALS=/ssdwork/jelber2/rfs/rfs.immunome.interval.list \
METRIC_ACCUMULATION_LEVEL=SAMPLE \
R=/ssdwork/jelber2/rfs/AmexG_v3.0.0.fa \
I=ALL-samples-RG.bam \
O=ALL-samples-coverage-metrics.txt
Best,
Gopo

Last edited by Gopo; 08-08-2018 at 11:12 PM. Reason: wrong syntax for displaying code
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Old 08-11-2018, 06:48 PM   #5
anoopkmr
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This tools helps me create bed files from a gene list:
https://genome-euro.ucsc.edu/cgi-bin/hgTables

Choose bed format while downloading.
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