Hi,
Is there any way to modify a SAM/BAM in order to have real reads replaced by the perfect reads(replacing wrong bases with the right bases in the ref) ?
for example:
REF : ACTGTGTCCTGTACTG
READ: TCTGTGTCCTTTACTG
the REF sequence will be showed instead of the real read.
One solution is to fetch the postion of each read(chr:start-end) and fetch the proprer reads from the reference but i'm wondering if there's a better way to do that directely using samtools/awk ?
The desired output is bam or fastq
Thanks in advance
Best,
Ramzi
Is there any way to modify a SAM/BAM in order to have real reads replaced by the perfect reads(replacing wrong bases with the right bases in the ref) ?
for example:
REF : ACTGTGTCCTGTACTG
READ: TCTGTGTCCTTTACTG
the REF sequence will be showed instead of the real read.
One solution is to fetch the postion of each read(chr:start-end) and fetch the proprer reads from the reference but i'm wondering if there's a better way to do that directely using samtools/awk ?
The desired output is bam or fastq
Thanks in advance
Best,
Ramzi
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