Hello
Say you have a BAM file produced by dorado with reads having different dx tags (1, 0, or -1)
If you do :
samtools fastq -d dx:1 -d dx:0 BAMFILE
samtools view -d dx:1 -d dx:0 BAMFILE | samtools fastq
You are not getting the same output. It seems that the -d option within the fastq mode only considers the latest -d call, while the view mode aggregates all the calls. The latest sound much better...
Regards,
Version:
samtools 1.18
Using htslib 1.18
Hello
Say you have a BAM file produced by dorado with reads having different dx tags (1, 0, or -1)
If you do :
samtools fastq -d dx:1 -d dx:0 BAMFILE samtools view -d dx:1 -d dx:0 BAMFILE | samtools fastqYou are not getting the same output. It seems that the -d option within the fastq mode only considers the latest -d call, while the view mode aggregates all the calls. The latest sound much better...
Regards,
Version:
samtools 1.18
Using htslib 1.18