how to get perfects aligned reads instead of real read

[ramouz87]

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

[nilshomer]

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

Use the cigar field and the MD tag (if available) to convert the read into the reference without having to search a reference FASTA file. I will leave it to you as an exercise, though you can checkout the bio-samtools (written in perl).