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mozack / abra

Assembly Based ReAligner
MIT License
71 stars 12 forks source link

somatic mode #9

Closed joonlee3 closed 10 years ago

joonlee3 commented 10 years ago

As suggested in README, I was trying to realign tumor/normal bam together. I found that ABRA generated a realigned bam file only for a given tumor bam. Does ABRA not generate a re-aligned bam file for a normal bam? or Did I miss something?

My command: java -Xmx16g -jar ${ABRA_JAR} \ --in ${tumour_id}.all.sorted.dedup.bam ${normal_id}.all.sorted.dedup.bam \ --out ${tumour_id}.all.sorted.dedup.realigned.bam ${normal_id}.all.sorted.dedup.realigned.bam \ --ref ${reference_genome} \ --targets ${!target_bed_file_path} \ --threads 4 --mad ${mad} --mbq ${mbq} \ --working ${temp_dir}

Thank you, Joon

mozack commented 10 years ago

Please separate the bam files with commas (,) and no whitespace.

i.e. --in ${tumour_id}.all.sorted.dedup.bam,${normal_id}.all.sorted.dedup.bam \ --out ${tumour_id}.all.sorted.dedup.realigned.bam,${normal_id}.all.sorted.dedup.realigned.bam \