Hi,
Sorry for the newbie question!
I am trying to convert output from HiSeq whole genome sequence to bam format that will be used by GATK. For any one sample, I have multiple files, e.g.
C12XXZ_s1_1_SL123.fastq.gz
C12XXZ_s1_2_SL123.fastq.gz
.
.
C12XXZ_s8_1_SL123.fastq.gz
C12XXZ_s8_2_SL123.fastq.gz
.
.
A456ZXX_s1_1_SL123.fastq.gz
A456ZXX_s1_2_SL123.fastq.gz
.
.
A456ZXX_s8_1_SL123.fastq.gz
A456ZXX_s8_2_SL123.fastq.gz
Do I need to separately combine each lane forward and reverse reads into a bam file (i.e I will get C12XXZ_s1.bam, C12XXZ_s2.bam,….A456ZXX_s1.bam, A456ZXX_s2.bam) and then just to concatenate all these files to get one bam for the sample?
thanks!
Sorry for the newbie question!
I am trying to convert output from HiSeq whole genome sequence to bam format that will be used by GATK. For any one sample, I have multiple files, e.g.
C12XXZ_s1_1_SL123.fastq.gz
C12XXZ_s1_2_SL123.fastq.gz
.
.
C12XXZ_s8_1_SL123.fastq.gz
C12XXZ_s8_2_SL123.fastq.gz
.
.
A456ZXX_s1_1_SL123.fastq.gz
A456ZXX_s1_2_SL123.fastq.gz
.
.
A456ZXX_s8_1_SL123.fastq.gz
A456ZXX_s8_2_SL123.fastq.gz
Do I need to separately combine each lane forward and reverse reads into a bam file (i.e I will get C12XXZ_s1.bam, C12XXZ_s2.bam,….A456ZXX_s1.bam, A456ZXX_s2.bam) and then just to concatenate all these files to get one bam for the sample?
thanks!
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