Extract Hard-clipped and soft-clipped values from fifth column

Question

[Ram]

Hello all,

Is it possible to know how I can extract 105 hard-clipped base from fifth column and then add value 105 to end coordinate of chr1 ?

As I tried with awk, but no success !

chr1    21730812    21730857    M00758:777:BKR4B:1:2103:25646:13282  45M105H
chr1    179196680   179196716     M00758:777:BKR4B:1:2101:24687:24458     87H36M27H

Thanks a lot!

[Bastien Hervé]

This is your input :

chr1    21730812    21730857    M00758:777:BKR4B:1:2103:25646:13282    45M105H

chr1    179196680    179196716    M00758:777:BKR4B:1:2101:24687:24458    87H36M27H

And you want a result like this :

chr1    21730812    21730962    M00758:777:BKR4B:1:2103:25646:13282    45M105H

chr1    179196680    179196743    M00758:777:BKR4B:1:2101:24687:24458    87H36M27H

?

[Ram]

I want a result like this :

chr1   21730857     21730962    M00758:777:BKR4B:1:2103:25646:13282    45M105H

chr1    179196716    179196743    M00758:777:BKR4B:1:2101:24687:24458    87H36M27H

Thanks !

[Bastien Hervé]

You mean for the first line :

chr1   21730812     21730962    M00758:777:BKR4B:1:2103:25646:13282    45M105H

Because 45M105H does not have hard clipping as start

[Ram]

Yes ! Any idea how i can be able to achieve this ?

[Ram]

Please explain your awk script as it does nothing to pick relevant parts of $5 or add to $2 or $3. I don't even see why a loop is necessary in your awk script.

Also, please edit your question and add your awk script in there.

[Ram]

You wish to add number of Matched based to start position and number of hard clipped to end position?

Why?

[Pierre Lindenbaum]

I tried with awk

show us the awk code

[Pierre Lindenbaum]

105 hard-clipped base from fifth column and then add value 105 to end coordinate of chr1 ?

do you really want to do this ??? how would you handle a 'N' or a 'D' in the cigar string ???

[Ram]

Here is the code :

awk -F'\t' 'NR==FNR{arr[$1]++;next}{for(i=1; i<=NF; i++) if ($i in arr){a[i]++;}} { for (i in a) printf "%s\t", $i; printf "\n"}'  file.bed

[Pierre Lindenbaum]

can you please explain this awk script ?

[d-cameron]

What is the larger problem that you are attempting to solve, and why only hard clips, not soft clips?

Wouldn't it be easier to just use a utility such as gridss.ComputeSamTags SOFTEN_HARD_CLIPS=true to convert your hard clips into soft clips then do you conversion to BED?

[Ram]

Hello Ram,

Please provide feedback to the comments here so we can get this discussion to closure.

Thank you!