Question: Samtools mpileup degenerative characters
1
gravatar for bruseq
17 months ago by
bruseq20
bruseq20 wrote:

Hello everyone,

I am using samtools to get mpileup file.

but there is an degenerative characters "-1y, -1Y, -1s" etc. also shown in the mpileup file.

I want to know why these degenerative characters are shown in mpileup file.

Please help me to sort the above problem.

Thanks,

Divya

ADD COMMENTlink modified 5 months ago by swbarnes24.5k • written 17 months ago by bruseq20
1

I have not seen such characters myself - perhaps it is a new feature of sorts. For now to avoid confusion you should post the command and the output that you are getting. Just to make sure that it is not something else.

ADD REPLYlink written 17 months ago by Istvan Albert ♦♦ 78k

Thanks for your reply,

I m using samtools version 0.1.19-96b5f2294a

Here below I m posting the command

samtools mpileup -f ref_genome.fa input.bam > output.mpileup

Error lines

2   3616324 A   211 .,,.,..,-1y...,..,,..............,,,,,,......,,,...,,,....,,,....,,,,,,,.....,,..,.......,.........,,,..........,,,,,,,,,,,,,,.,,,,..,,,,.,..,.....,,,,.,,,....,...,.....,...................^!.^$.^$.^*.^!.^*.^$.^$.^!.^!.^!.^2.^$.^!.^!.^!.^!.^!.^2.^$.^$.^!.^!.^!.^$.    FFFFFFFBFFFFFFIIFFFFFFFBFFFFBFIIIIIIIF<FFFIIIFFFIIIIFIFIIIIFIIIIFIIIII:IIIIIIIIIII8FIIIIIIIIFIIIIIIIIFFIIFIFIFFIIFIIIFBIIFIIIFBIIFIIIFIIIIIIIIIIFFBFIFFFIIFIFFFFFF;:::::====8=============BBBBBBBBBBBBBBBBBBBB9BBBB 
2   3623671 A   1208 ,$.$..$..,,,$,,,$,,,.,,,,,,,,,.,,,,,.,....,,,,,,$,,,,,,,$,,,,,,,,,,,,,....,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,..,,,,,,,,,,,,,,,,,,,,,,,,,,g,,,,...,,,,,,,.....,,,,,,-1s,,,,,,,,,,,,,,,,,,,,,,,,,,..,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,..,,,,,,,,,,,,,,,,,,,,,,,,,.....,,,,,,,,,,,,,,..,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,..,,,,,,,,,,,,,,,,,,,,.,,,,,,,,,..,,,,,,.,,,,,,...........,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,..,,,..,,,,,,,,,...,,,.........,,,,,,,,,......,,,,,.,,,,,,,,,,,,......,,,,,,,,,,,,,,,.....,,,,,,,,..,,,,,,,.....,,,,,,,,,......,,,,,.,,,,,,,,,,,,,,,..,,,,,,,...,,,,...,,,,....,,,,,,.....................,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.........,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.....,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.................,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.........,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,..,,,,,,,,,,,,,,,,,,,,,,,,,......,,,,,,,,,.,,,,,,,,,,,,...,,,..,,,,,,,,,.,,,,,,,,...,,,,,,,,,,,....,,,,,,,,,,,..,,,,,,,.,,,,,,,,.,,,,.,,,,,..,,,,,,.,,,,,,,,.,,...,,,,,,,,..,,,,,,,,,,,,,,,,,,,,,..,,,,,,,,,,,,..,,,,,...,,,,,,,,,,,....,,,,,,,.......,,,,,,,,,,.,,,,,,,....,,,,,,,,....,,,,,,,,,,.,,..,.,,...,,,,,....,,,.,,,,,,.,,,,,.,^!.   ;;F;F;BBBBBBBBBF4BBBBBBBFFFFFFFFFFFFBFFFBBBFBFFBFBFFFFFF<FFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFBBFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFBFFFF<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFF<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFBFFFFBFFFFFFFFFFFFFBFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFFFBFFF<FFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFF/FF<FFFFFFFF<FBFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFB<FFFFFBFF//FFFFFFFFFFFFFFFFFFFFFFFF<FBFFFFFFF<FFFFFFFFFFFFFBFFFFFFFFFFFFBFBFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFBFFFF/FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFF9FFFFFFFFFFFFBFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFBFFF/FFFBFFFFFF/FFFFFFFFFFFFFFFFFFFFFFFFF<FBFFFFFFFFFFFFFFFFBBFFFFFFFFFFBFFFFFFFFFFFFFFFFFFBFF<FFFFFFFFFFFFFFF<FFFFFFFF<FFBFF/FFFFFFFFFFFFFFF<FFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFBFFFFFFFBFFFFFFFFFFFBF<FFFFFBFFFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFBFF/FFFBFFBFFFFF/FFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFF/FBBFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFF<FFFFFFFFFFBFFFFFFFFFFFFFFFF/FFFFFFFFFBFFFFFFFFFF<FFF7<FFFFFFFBFFFFFFFBFFFFFFB<FBFFB/B
ADD REPLYlink modified 17 months ago by Istvan Albert ♦♦ 78k • written 17 months ago by bruseq20

samtools 0.1.19-96b5f2294a looks like a more than four years old (basically ancient) version of the tool - addition you see that 96b5f2294a that is also pretty weird.

The current version is 1.5 see if that version of samtools mpileup does the same.

ADD REPLYlink modified 17 months ago • written 17 months ago by Istvan Albert ♦♦ 78k

Hello sir,

Now I installed samtools version-1.5 but the problem is persist in the mpileup file. Any suggestion.

ADD REPLYlink written 17 months ago by bruseq20

Looks like they could be indels.

ADD REPLYlink written 17 months ago by Samuel Brady260

Thanks for the comment @ Saumel

That I know the -1 are the indels but I didn't get why these "y" and "s" characters also encounter with -1 in the mpileup file.

ADD REPLYlink modified 17 months ago • written 17 months ago by bruseq20

The manual does not mention these charcaters so it is quite the head scratcher.

http://www.htslib.org/doc/samtools.html

I would open an issue on the github page to ask for clarification (and you can reference this post in the issue).

https://github.com/samtools/samtools/issues

(and please come back and let us know what the resolution is)

ADD REPLYlink written 17 months ago by Istvan Albert ♦♦ 78k

To throw in an idea: Aren't y and s IUPACs that are present if two or more nucleotides are to be represented? But I do not know enough about the pileup format to say if that makes sense t this context here.

ADD REPLYlink modified 15 months ago • written 15 months ago by ATpoint10k
0
gravatar for swbarnes2
5 months ago by
swbarnes24.5k
United States
swbarnes24.5k wrote:

Maybe your reference has a Y at that position, and your reads have a 1 base deletion right there.

ADD COMMENTlink modified 5 months ago • written 5 months ago by swbarnes24.5k
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