Improve error message for no bridge found

[jsgounot]

Hi,

I run Gretel on different datasets. I've got this error message :

[FAIL] Unable to recover pairwise evidence concerning SNP #15 at position 1077
Gretel needs every SNP to appear on a read with at least one other SNP, at least once.
There is no read in your data set that bridges SNP #15 with any of its neighbours.

However, when I look at my datafile with IGV, I can see multiple reads which have 2 SNPs : screenshot

Am I missing something ?
Thanks !

[SamStudio8]

Hi Jean, There should be a table that gets dumped out that shows all the observed SNP pairs, what does that show around SNP 15? Sam

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On Wed, 25 Nov 2020, 10:10 GOUNOT Jean-Sebastien, ***@***.***> wrote: Hi, I run Gretel on different datasets. I've got this error message : [FAIL] Unable to recover pairwise evidence concerning SNP #15 <#15> at position 1077 Gretel needs every SNP to appear on a read with at least one other SNP, at least once. There is no read in your data set that bridges SNP #15 <#15> with any of its neighbours. However, when I look at my datafile with IGV, I can see multiple reads which have 2 SNPs : screenshot <https://imgur.com/a/3IVVRos> Am I missing something ? Thanks ! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#34>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAIN6OXMZPYSICJA5HO4XJ3SRTJYLANCNFSM4UCFXCZA> .

[jsgounot]

Do you mean the one produced by --dumpsnps ?

13	969	969
14	1032	1032
15	1077	1077
16	1206	1206
17	1230	1230

Edit : If you want, here is an example with bam and vcf files. Not exactly the same data set but it produces to the same error message. The command line : gretel Ecoli-Merged-K12.bam Ecoli-Merged-K12_variants_2.cgretel.vcf.gz NC_000913.3 -s 1 -e 10000 &> log.txt.

[SamStudio8]

Sorry for the confusion - it seems that table doesn't get printed if that particular error is found! The VCF you are using, what is the position of SNP 14 and SNP 16? It would seem one side is not bridged by a read.

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On Wed, Nov 25, 2020 at 12:47 PM GOUNOT Jean-Sebastien < ***@***.***> wrote: Do you mean the one produced by --dumpsnps ? 13 969 969 14 1032 1032 15 1077 1077 16 1206 1206 17 1230 1230 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#34 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAIN6ORX7UEPDEC6TPYLGX3SRT4EPANCNFSM4UCFXCZA> .

[jsgounot]

I just check with IGV, SNP 15 is linked to 14 but not to 16. However, 16 is linked to 17. So I guess that all consecutive pairs of SNPs must have at least one shared read?

[SamStudio8]

Ah yes, Gretel requires all adjacent pairs must be bridged at least once (but ideally a little more)

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On Fri, 27 Nov 2020, 01:47 GOUNOT Jean-Sebastien, ***@***.***> wrote: I just check with IGV, SNP 15 is linked to 14 but not to 16. However, 16 is linked to 17. So I guess that all consecutive pairs of SNPs must have at least one shared read? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#34 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAIN6OU2DNFHGPASWSKBYJ3SR4AMVANCNFSM4UCFXCZA> .

[jsgounot]

Ok I've been a bit confused by the error message then. Thanks for the help.

[SamStudio8]

Understood! I'll try and improve that message.

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On Fri, 27 Nov 2020, 08:21 GOUNOT Jean-Sebastien, ***@***.***> wrote: Ok I've been a bit confused by the error message then. Thanks for the help. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#34 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAIN6OT6XMF3LK4C4CHY2ILSR5OO7ANCNFSM4UCFXCZA> .