What situation will causal annovar take a variants as "invalid_input" ?

[Shicheng-Guo]

Dear Prof. Wang,

What situation will cause ANNOVAR take a variants as "invalid_input" ?

If ANNOVAR encounters an invalid input line, it will write the invalid line into a file called .invalid_input

It looks if the SNPs are not existed in assigned "avsnp154", then they will be taken as invalid_input. but I still want to make sure.

Thanks.

Shicheng

[kaichop]

invalid_input means the input line is invalid. It is not relevant to whether it is in avsnp154 or not. You can print out the file and see what is in the file and check why they are invalid input.

On Fri, Jun 11, 2021 at 2:25 PM Shicheng Guo @.***> wrote:

Dear Prof. Wang,

What situation will causal annovar take a variants as "invalid_input" ?

If ANNOVAR encounters an invalid input line, it will write the invalid line into a file called .invalid_input

It looks if the SNPs are not existed in assigned "avsnp154", then they will be taken as invalid_input. but I still want to make sure.

Thanks.

Shicheng

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[Shicheng-Guo]

for example, here are some examples will be showed in *.invalid_input

17      44349158        44349158        GCAGA   G
17      44349407        44349407        AT      A
17      44349413        44349413        CCTGT   C
17      44349603        44349603        TC      T
17      44350229        44350229        TAAC    T
17      44350262        44350262        TAGTC   T
17      44350272        44350272        GA      G
17      44350458        44350458        AC      A
17      44350538        44350538        CT      C
17      44350579        44350579        TGAG    T
17      44350800        44350800        CGTGA   C
17      44350983        44350983        CCT     C
17      44351491        44351491        GCA     G
17      44351650        44351650        TGGA    T
17      44351733        44351733        CCCT    C
17      44351760        44351760        AC      A
17      44351798        44351798        ATATGG  A
17      44351806        44351806        GGGGACA G
17      44351829        44351829        AG      A
17      44351877        44351877        AG      A
17      44352006        44352006        AC      A
17      44352180        44352180        AGCTGCCCGGTGGGGCAGACCT  A
17      44352187        44352187        CG      C
17      44352300        44352300        GACAGGA G
17      44352420        44352420        AAGTGG  A
17      44352434        44352434        CA      C
17      44352522        44352522        CCTG    C
17      44352635        44352635        CCTCT   C
17      44352646        44352646        CCT     C
17      44352773        44352773        AC      A
17      44352814        44352814        ACT     A

[kaichop]

The format is wrong. For example, there are 5bp in ref, so the start and end position cannot be the same. You should manually change it so they differ by 4.

On Thu, Jun 17, 2021 at 11:52 PM Shicheng Guo @.***> wrote:

for example, here are some examples will be showed in *.invalid_input

17 44349158 44349158 GCAGA G 17 44349407 44349407 AT A 17 44349413 44349413 CCTGT C 17 44349603 44349603 TC T 17 44350229 44350229 TAAC T 17 44350262 44350262 TAGTC T 17 44350272 44350272 GA G 17 44350458 44350458 AC A 17 44350538 44350538 CT C 17 44350579 44350579 TGAG T 17 44350800 44350800 CGTGA C 17 44350983 44350983 CCT C 17 44351491 44351491 GCA G 17 44351650 44351650 TGGA T 17 44351733 44351733 CCCT C 17 44351760 44351760 AC A 17 44351798 44351798 ATATGG A 17 44351806 44351806 GGGGACA G 17 44351829 44351829 AG A 17 44351877 44351877 AG A 17 44352006 44352006 AC A 17 44352180 44352180 AGCTGCCCGGTGGGGCAGACCT A 17 44352187 44352187 CG C 17 44352300 44352300 GACAGGA G 17 44352420 44352420 AAGTGG A 17 44352434 44352434 CA C 17 44352522 44352522 CCTG C 17 44352635 44352635 CCTCT C 17 44352646 44352646 CCT C 17 44352773 44352773 AC A 17 44352814 44352814 ACT A

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