I have a query regarding Processing of Fastq to Ubam file and then to vcf.gz file, I followed the same gatk guideline for conversion of paired end fastq files to .unmapped.bam files. and then used that unmapped bam file as input to GOAST server for further processing of Ubam file to vcf.gz format. but ever time my automated gatk job for conversion of ubam to *.vcf.gz is failed. I think there is problem in assigning Read group name to both paired end fastq.gz files during conversion of raw unmapped fastq.gz files to uBam file. Please give suggestion regard this.
Dear Ashwani Kumar,
Please check this link.
https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/tutorials/6484-how-to-generate-an-unmapped-bam-from-fastq-or-aligned-bam
Best regards
Ashwani Kumar
These links might be useful, have a look:
1. https://gatk.broadinstitute.org/hc/en-us/articles/4403687183515--How-to-Generate-an-unmapped-BAM-from-FASTQ-or-aligned-BAM
2. https://gatk.broadinstitute.org/hc/en-us/articles/360039568932--How-to-Map-and-clean-up-short-read-sequence-data-efficiently
3. https://pos.strategictestingservice.com/34ztn/fastq-file-example-download.html
4. http://www.chem-structure.org/khkrgg/how-to-open-fastq-gz-file.html
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