One sample, is whole exome sequenced, twice to reach the required coverage as these samples had some issues. The sequencing in both sample is exactly same (batch, machine and the vendor) I wonder, if it makes sense to merge these two fastq files in order to reach the adequate coverage., and do variant calling once ?! if so, how should I merge them. is there any other suggestion in this case?
align your reads with bwa/bowtie2, etc... and don't forget to create a group to mark the origin of your fastqs. For BWA:
-R STR Complete read group header line. ’\t’ can be used in STR and will be converted to a TAB in the output SAM. The read group ID will be attached to every read in the output. An example is ’@RG\tID:foo\tSM:bar’. [null]
or you can use picard http://picard.sourceforge.net/command-line-overview.shtml#AddOrReplaceReadGroups
at one point , you can merge the BAMs using http://picard.sourceforge.net/command-line-overview.shtml#MergeSamFiles . You'll be aways be able to exclude/see the origin of the reads as they will carry a Group-ID.