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Samtools mpileup degenerative characters

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

samtools mpileup degenrative characters
• 3,501 views • link
updated by swbarnes2 swbarnes2 • written by bruseq • bruseq

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.

• 0 views • link
written by Istvan Albert Istvan Albert

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
• 0 views • link
updated by Istvan Albert Istvan Albert • written by bruseq • bruseq

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.

• 0 views • link
written by Istvan Albert Istvan Albert

Hello sir,

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

• 0 views • link
written by bruseq • bruseq

Looks like they could be indels.

• 0 views • link
written by Samuel Brady Samuel Brady

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.

• 0 views • link
written by bruseq • bruseq

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.

• 0 views • link
written by ATpoint ATpoint

1 answer

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

• 1 views • link
written by swbarnes2 swbarnes2

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