merge multpile bam files for unique samples

Question

[ifudontmind_plzz]

I want to merge multiple bam files for each unique samples. I have a list with names of bam files corresponding to each sample ID.

Name    ID
SC_R2   AD_1
SC_R3   AD_1
SC_C1   AD_2
SC_C2   AD_2
SC_C3   AD_2

[Sukhi Singh]

So what is the question? Please frame your question properly and what have to tried to achieve it to get good answers.

[ifudontmind_plzz]

Sorry for not being clear.

I downloaded sequencing results (.bam file) for 27 samples from EGA. There are around 400 bam files in total, which has to be merged. I have a list with names of bam files in one column and its corresponding sample ID in other column. I would like to merge these bam files so that finally I have 27 bam files (one bam file for each samples).

For example from the table, there are 5 bam files which corresponds to 2 samples,

AD_1 > SC_R2 + SC_R3

AD_2 > SC_C1 + SC_C2 + SC_C3

Hope I conveyed the message.

Answer 1

[A. Domingues]

Untested and taken advantage of what Devon already said:

info="description.tsv" # this is the file with the correspondence filename/sample_ID

# get the sample ID
sample_names=`cut -f2 $info | sort | uniq | tr "\n" " "`

for sample in $sample_names;
do
   bams=`grep $sample $info | cut -f1 | awk '{print $1".bam"}' | tr "\n" " "` # remove the awk statment if the suffix is already present
   echo "aligments for $sample are $bams"
   echo samtools merge $bams
done

# remove the echo in the 3rd line of the loop is testing is successful.

A bit over-elaborate but should do the trick.

[ifudontmind_plzz]

is this a bash script?

[Devon Ryan]

Yes, it is.

[A. Domingues]

What Devon said :)

Answer 2

[Devon Ryan]

samtools merge AD_1.bam SC_R2.bam SC_R3.bam
samtools merge AD_2.bam SC_C1.bam SC_C2.bam SC_C3.bam

You could also use wild cards, most likely. Of course, it's likely that there's a bunch of information that you've not mentioned about why the two simple commands that I wrote won't suffice...