I downloaded some TCGA ExomeSeq bam file and would like to convert them to fatsq. Picard can not convert them because there are some reads with identical same readname in the bam files. As suggested by the community bedtools bamtofastq can randomly choose only one of these reads and put it to fastq file. I tried bedtools bamtofastq but the duplicate read names are still in the fastq output.
My question is :
- Why there are reads with identical readname in bam files?
- How can I fix this issue? should I rename the reads name in fastq files?