Tool:Converting MUMmer snps file to a real VCF file

Question

[Matteo Schiavinato]

Hi all,

UPDATE:

the tool is now available as part of a growing set of tools that I called all2vcf. You can clone the repository from here:

https://github.com/MatteoSchiavinato/all2vcf

ORIGINAL:

For my own necessity I have recently made this tool that, contrary to the original mummer-2-vcf.pl script, converts the snps output of the show-snps MUMmer tool to a real VCF file (with header and the like).

https://github.com/MatteoSchiavinato/Utilities/blob/master/my-mummer-2-vcf.py

EDIT: please use the --input-header option if your input *.snps file has a header. Otherwise you will have an IndexError somewhere in the code.

It worked with my data, and it should work with yours. Anyone interested in giving it a test run?

[macielrodriguez2]

I'll try it right now! thank you so much for your contribution! I was looking exactly for some way to convert the output of my mummer snps to vcf :D

[moduff]

This would be very useful but it's not quite working for me.

I'm trying to compare 2 viral (30k) genomes.

I used MUMmer's nucmer and show-snps commands:

nucmer --prefilx=1000-X70047 nc_045512_wg.fasta 1000-X70047.fasta
show-snps -T 1000-X70047.delta > 1000-X70047.snps

The snps file looks like this:

/Users/moduff/Desktop/SARS2/nc_045512_wg.fasta /Users/moduff/Desktop/SARS2/1000-X70047.fasta
NUCMER

[P1]    [SUB]   [SUB]   [P2]    [BUFF]  [DIST]  [R]     [Q]     [FRM]   [TAGS]
8782    C       T       8383    8369    8383    0       0       1       1       NC_045512        X70047_consensus
17747   C       T       17348   111     12155   0       0       1       1       NC_045512       X70047_consensus
17858   A       G       17459   111     12044   0       0       1       1       NC_045512       X70047_consensus
18060   C       T       17661   202     11842   0       0       1       1       NC_045512       X70047_consensus
27525   A       G       27126   187     2377    0       0       1       1       NC_045512        X70047_consensus
28144   T       C       27745   619     1758    0       0       1       1       NC_045512        X70047_consensus

When I fed this to mummer-2-vcf.pl via

my-mummer-2-vcf.py -s 1000-X70047.snps -n --output-header --reference nc_045512_wg.fasta

I get this error message:

Traceback (most recent call last):
  File "my-mummer-2-vcf.py", line 313, in <module>
    Vcf_lines = [ convert_snps_to_vcf(line) for line in Lines ]
  File "my-mummer-2-vcf.py", line 313, in <listcomp>
    Vcf_lines = [ convert_snps_to_vcf(line) for line in Lines ]
  File "my-mummer-2-vcf.py", line 56, in convert_snps_to_vcf
    scaffold = lst[10]
IndexError: list index out of range

Any suggestions?

[Matteo Schiavinato]

Yes, please read through this github issue that I closed some weeks ago, I believe it's the same issue :)

https://github.com/MatteoSchiavinato/Utilities/issues/1

(to improve readability, could you wrap the code parts of your answer inside a code block?)

[Alish]

Hi, I seem to be getting the same error even though I used -T with my show-snps. Was this error ever resolved/confirmed?

[CoolEvilgenius]

Thank you for your practical code!

[Diana Carolina]

I converted my .snp file to .vcf without problems, later I tried to filter with the .vcf as an input but the Qual column appears empty. Do I have to do anything before filtering?. Many thanks for your code.

INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."
CHROM POS ID REF ALT QUAL FILTER INFO
NW_003020038.1 240 . A AG . . INDEL scaffold2:2512040 NW_003020038.1 240 . A AA . . INDEL scaffold2:2512041 NW_003020038.1 240 . A AC . . INDEL scaffold2:2512042 NW_003020038.1 240 . A AC . . INDEL scaffold2:2512043 NW_003020038.1 240 . A AG . . INDEL scaffold2:2512044 NW_003020038.1 240 . A AA . . INDEL scaffold2:2512045 NW_003020038.1 281 . a aA . . INDEL scaffold2:2511996 NW_003020038.1 281 . a aA . . INDEL scaffold2:2511997 NW_003020038.1 281 . a aG . . INDEL scaffold2:2511998 NW_003020038.1 391 . aTT a . . INDEL scaffold2:2511886 NW_003020038.1 394 . T A . . . scaffold2:2511886 NW_003020038.1 493 . C T . . . scaffold2:2511787 NW_003020038.1 1393 . G A . . . scaffold2:2510887 NW_003020038.1 1395 . G T . . . scaffold2:2510885 NW_003020038.1 1875 . C T . . . scaffold2:2510405 NW_003020038.1 1881 . G A . . . scaffold2:2510399 NW_003020038.1 2336 . G C . . . scaffold2:2509944 NW_003020038.1 2882 . t tT . . INDEL scaffold2:2509394

[Matteo Schiavinato]

Hi, I am not sure you can carry on any type of quality from mummer snps to a VCF file. Do you have any quality indication in your snps file?

[Diana Carolina]

Hi Matteo

This my .snps file.

[P1]  [SUB]  [SUB]    [P2][BUFF]  [DIST] [R]    [Q]     [FRM]   [TAGS]
241 .   G   2512040 0   241 0   0   1   -1  NW_003020038.1  scaffold2
241 .   A   2512041 0   241 0   0   1   -1  NW_003020038.1  scaffold2
241 .   C   2512042 0   241 0   0   1   -1  NW_003020038.1  scaffold2
241 .   C   2512043 0   241 0   0   1   -1  NW_003020038.1  scaffold2
241 .   G   2512044 0   241 0   0   1   -1  NW_003020038.1  scaffold2
241 .   A   2512045 0   241 0   0   1   -1  NW_003020038.1  scaffold2
282 .   A   2511996 0   282 0   0   1   -1  NW_003020038.1  scaffold2
282 .   A   2511997 0   282 0   0   1   -1  NW_003020038.1  scaffold2
282 .   G   2511998 0   282 0   0   1   -1  NW_003020038.1  scaffold2
392 T   .   2511886 1   392 0   0   1   -1  NW_003020038.1  scaffold2
393 T   .   2511886 1   393 0   0   1   -1  NW_003020038.1  scaffold2
394 T   A   2511886 1   394 0   0   1   -1  NW_003020038.1  scaffold2
493 C   T   2511787 99  493 0   0   1   -1  NW_003020038.1  scaffold2
1393    G   A   2510887 2   1393    0   0   1   -1  NW_003020038.1  scaffold2