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bioinform / somaticseq

An ensemble approach to accurately detect somatic mutations using SomaticSeq
http://bioinform.github.io/somaticseq/
BSD 2-Clause "Simplified" License
192 stars 53 forks source link

Fastq2bam #62

Closed esherafat closed 6 years ago

esherafat commented 6 years ago

Hello, Can you please upload the "fastq2bam_pipeline_singleThread.sh" script? It is a requirement for running " somaticseq/utilities/dockered_pipelines/alignments/fastq2bam_pipeline.sh". Thanks!

litaifang commented 6 years ago

fastq2bam_pipeline.sh is just a script to align FASTQ files into BAM files based on GATK's best practices, i.e., bwa mem, mark duplicates, GATK indel realignment, and BQSR. If you start with BAM files, there is no need to run any of those scripts.

litaifang commented 6 years ago

I assume the issue is solved. Feel free to re-open if you still have questions.