https://github.com/tomwhite/bamreport
Produce a report on a BAM file listing useful information
https://github.com/tomwhite/bamreport
bam bioinformatics genomics ngs
Last synced: 4 days ago
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Produce a report on a BAM file listing useful information
- Host: GitHub
- URL: https://github.com/tomwhite/bamreport
- Owner: tomwhite
- Created: 2018-04-05T11:14:55.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2018-04-05T11:15:08.000Z (over 7 years ago)
- Last Synced: 2025-01-17T21:43:53.335Z (9 months ago)
- Topics: bam, bioinformatics, genomics, ngs
- Language: Java
- Size: 116 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
```
BAM=/Users/tom/workspace/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam
~/sw/bedtools2/bin/bedtools genomecov -ibam $BAM -bga > bam.bedgraph
```
From http://seqanswers.com/forums/showpost.php?p=116995&postcount=11
```
DICT=/Users/tom/workspace/gatk/src/test/resources/large/human_g1k_v37.20.21.dict
grep '@SQ' $DICT | tr ':' '\t' | awk -v OFS='\t' '{print $3, $5}' > $DICT.genome
~/sw/bedtools2/bin/bedtools makewindows -g $DICT.genome -w 1000000 \
| ~/sw/bedtools2/bin/bedtools coverage -a - -b $BAM -counts > $BAM.counts.txt
````
bedtools coverage -hist -abam $BAM
----
```bash
mvn compile
mvn exec:java -Dexec.mainClass=com.cloudera.bamreport.BamReport -Dexec.args="/Users/tom/workspace/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam"
# unmapped BAM
mvn exec:java -Dexec.mainClass=com.cloudera.bamreport.BamReport -Dexec.args="/Users/tom/workspace/gatk/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/QualityScoreDistribution/unmapped.bam"
```
Sparklines
```bash
mvn compile
mvn -q exec:java -Dexec.mainClass=com.cloudera.bamreport.BamCoverageSparkline -Dexec.args="/Users/tom/workspace/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam" > sparkline.html
open sparkline.html
```