Hi all，
For testing the indel calling precision of Dindle, SAMtools and GATK, we simulated indels and SNPs at a 1:9 ratio. Than we considered the base-calling error by using the MAQ to generate pair-end reads. After that I don't know how to generate Sequencing indel errors.
If we generate some indels in the reads, that would cause the inequality of reads' length. MAQ can only add 1bp sequencing indel errors according to the manual.
How to add some sequencing indel errors(1-5bp) to our simulation data? Should we add some sequencing indel errors when generating reads or after generation of reads ?
Thanks a lot.
For testing the indel calling precision of Dindle, SAMtools and GATK, we simulated indels and SNPs at a 1:9 ratio. Than we considered the base-calling error by using the MAQ to generate pair-end reads. After that I don't know how to generate Sequencing indel errors.
If we generate some indels in the reads, that would cause the inequality of reads' length. MAQ can only add 1bp sequencing indel errors according to the manual.
How to add some sequencing indel errors(1-5bp) to our simulation data? Should we add some sequencing indel errors when generating reads or after generation of reads ?
Thanks a lot.