This tools helps me create bed files from a gene list:
Choose bed format while downloading.
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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
Gopo
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[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
# reference genome is AmexG_v3.0.0.fa
# generate fasta index
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 you need to add read groups
java -Xmx64g -jar ~/bin/picard-2.18.10.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
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
[\CODE]
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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 # reference genome is AmexG_v3.0.0.fa # generate fasta index 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 you need to add read groups java -Xmx64g -jar ~/bin/picard-2.18.10.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 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
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So, you will have to generate the BED file yourself based on the coordinates of the genes or exons that you are interested in.
Code:# generate fasta index for genome (genome 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
Code:java -Xmx64g -jar ~/bin/picard.jar AddOrReplaceReadGroups \ I=ALL-samples-recal-no-read-groups.bam \ O=ALL-samples-recal-no-read-groups-for-callableloci.bam \ SORT_ORDER=coordinate \ RGPL=illumina \ RGPU=barcode \ RGLB=Lib1 \ RGID=all \ RGSM=all \ VALIDATION_STRINGENCY=LENIENT
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Originally posted by Gopo View PostTry CollectHSmetrics - part of Picard Tools
For details see:
https://broadinstitute.github.io/pic...-overview.html
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Try CollectHSmetrics - part of Picard Tools
For details see:
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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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