You can add the read group directly in bowtie2:
bowtie2 -x bowtie2_index_hg38 --rg-id sample1 --rg SM:sample1 ... |
samtools view -Su - | samtools sort - output
Picard's BuildBamIndex tool might be able to take input from a pipe (I'm
pretty sure this doesn't work with samtools at the moment), in which case:
... | picard SortSam INPUT=/dev/stdin OUTPUT=/dev/stdout | tee
output.bam | picard BuildBamIndex INPUT=/dev/stdin OUTPUT=output.bam.bai
Or something along those regards. I really can't recommend doing this,
though. Getting the index in an additional step is going to be a
minuscule time savings.
Devon
On 11/20/2015 08:21 PM, Yaseen Ladak wrote:
Hi All,
I need some help I want to pipe the output from samtools to picard
readgrous commands but I am failing:
*bowtie2 -x bowtie2_index_hg38 -1 R1.fq.gz -2 R2.fq.gz | samtools view
-Shb - | samtools sort - output*
What I want to achieve is the following is to also add the read groups
the output.bam file from above command and also index the output bam
file with reads groups. I am failing with the following command and I
dont know how to also index the output bam file that has the read group.
*bowtie2 -x bowtie2_index_hg38 -1 mrg_sample_1_R1_val_1.fq -2
mrg_sample_1_R2_val_2.fq | samtools view -Shb - | samtools sort - - |
picard AddOrReplaceReadGroups I= output.bam O=rg_output.bam
RGID=sample_1 RGLB=sample_1 RGPL=illumina_hi-seq RGPU=sample_1
RGSM=sample_1*
Can someone please help me?
Thanks,
Yaseen
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