Samtools mpileup degenerative characters

Question

[bruseq]

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

[Istvan Albert]

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.

[bruseq]

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

[Istvan Albert]

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.

[bruseq]

Hello sir,

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

[Samuel Brady]

Looks like they could be indels.

[bruseq]

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.

[Istvan Albert]

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)

[ATpoint]

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.

Answer 1

[swbarnes2]

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