Ad not in list

[DiyaVaka]

After running mity call i tried running mity normalise and it says AD not in list. I checked the vcf file produced by freebayes and it does not have AD. How to resolve this?

Thanks

DIya

[drmjc]

Hi, I have not experienced this. Can you provide a reproducible example and the command line that you used? thanks.

[master-noddy]

I also got this error, not able to resolve it.
Please see the command and the output

time mity call --reference hg38 --prefix DEMO --normalise 21A0003630-21IN000470_60307-CREV3_recal.cram.bam 21A0001020-21IN000165_59412-CREV3_recal.cram.bam --out-folder-path output/ --debug mity version 0.3.0
Calling mitochondrial variants
Running FreeBayes in sensitive mode
Traceback (most recent call last):
File "/root/anaconda3/envs/mity/bin/mity", line 29, in
args.func(args)
File "/root/anaconda3/envs/mity/lib/python3.7/site-packages/mitylib/commands.py", line 54, in _cmd_call
args.out_folder_path, args.region)
File "/root/anaconda3/envs/mity/lib/python3.7/site-packages/mitylib/call.py", line 108, in do_call
vcfnorm(vcf=unnormalised_vcf_path, out_file=output_file_name, p=p, genome=genome)
File "/root/anaconda3/envs/mity/lib/python3.7/site-packages/mitylib/normalise.py", line 1313, in do_normalise
single_allele = split_multi_allelic(variants)
File "/root/anaconda3/envs/mity/lib/python3.7/site-packages/mitylib/normalise.py", line 233, in split_multi_allelic
AD_idx = FORMAT_name.index("AD")
ValueError: 'AD' is not in list

[drmjc]

Hi, can you share your bam files, preferably just those ones with reads in chrM, so I can reproduce this error? Thanks

[DiyaVaka]

Hi, My error was resolved after I had a supported version of freebayes installed. Dedeepya Vaka Bioinformatics Programmer IV Institute of Human Genetics 513 Parnassus Ave., HSE S965E San Franscisco, CA 94143 W 415-502-3570 ***@***.***

…

________________________________ From: Mark Cowley ***@***.***> Sent: Monday, July 19, 2021 3:59 AM To: KCCG/mity ***@***.***> Cc: Vaka, Dedeepya ***@***.***>; Author ***@***.***> Subject: Re: [KCCG/mity] Ad not in list (#7) Hi, can you share your bam files, preferably just those ones with reads in chrM, so I can reproduce this error? Thanks — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or ‍ ‍ ‍ ‍ ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd Hi, can you share your bam files, preferably just those ones with reads in chrM, so I can reproduce this error? Thanks — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/KCCG/mity/issues/7*issuecomment-882452312__;Iw!!LQC6Cpwp!-yIJL9bT5z8WcalCGF-f9pd9zSx_BWWuUcD47S0lCcLbnR_GMVos-ifrKDdxw3NNn17q$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABHT2SNW5VD2T6UZNPKMMW3TYQAPZANCNFSM4XVQQAJA__;!!LQC6Cpwp!-yIJL9bT5z8WcalCGF-f9pd9zSx_BWWuUcD47S0lCcLbnR_GMVos-ifrKDdxw1nAOzkP$>.

[drmjc]

Great, thanks for letting me know. I'm curious what version threw the error? Thanks

…

On Tue, 20 Jul 2021, 12:05 am DiyaVaka, ***@***.***> wrote: Hi, My error was resolved after I had a supported version of freebayes installed. Dedeepya Vaka Bioinformatics Programmer IV Institute of Human Genetics 513 Parnassus Ave., HSE S965E San Franscisco, CA 94143 W 415-502-3570 ***@***.*** ________________________________ From: Mark Cowley ***@***.***> Sent: Monday, July 19, 2021 3:59 AM To: KCCG/mity ***@***.***> Cc: Vaka, Dedeepya ***@***.***>; Author ***@***.***> Subject: Re: [KCCG/mity] Ad not in list (#7) Hi, can you share your bam files, preferably just those ones with reads in chrM, so I can reproduce this error? Thanks — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or ‍ ‍ ‍ ‍ ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd Hi, can you share your bam files, preferably just those ones with reads in chrM, so I can reproduce this error? Thanks — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://urldefense.com/v3/__https://github.com/KCCG/mity/issues/7*issuecomment-882452312__;Iw!!LQC6Cpwp!-yIJL9bT5z8WcalCGF-f9pd9zSx_BWWuUcD47S0lCcLbnR_GMVos-ifrKDdxw3NNn17q$>, or unsubscribe< https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABHT2SNW5VD2T6UZNPKMMW3TYQAPZANCNFSM4XVQQAJA__;!!LQC6Cpwp!-yIJL9bT5z8WcalCGF-f9pd9zSx_BWWuUcD47S0lCcLbnR_GMVos-ifrKDdxw1nAOzkP$ >. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAEQQM2RPDZN5ML2ATJUVDDTYQWJDANCNFSM4XVQQAJA> .

[Pharmacogenetecist]

I am getting a similar issue trying to run one of the test files:
(MITY) mity call --prefix ashkenazim --out-folder-path "/Mity/testOUT/" --region MT:1-500 --normalise "/Mity/test_in/HG002.hs37d5.2x250.small.MT.RG.bam"
Found dependency: /anaconda3/envs/MITY/bin/freebayes
Found dependency: /anaconda3/envs/MITY/bin/gsort
Found dependency: /anaconda3/envs/MITY/bin/tabix
Found dependency: /anaconda3/envs/MITY/bin/bgzip
Found dependency: /anaconda3/envs/MITY/bin/python
Found dependency: /anaconda3/envs/MITY/bin/mity
mity version 0.4.0
Calling mitochondrial variants
Running FreeBayes in sensitive mode
Traceback (most recent call last):
File "/anaconda3/envs/MITY/bin/mity", line 29, in
args.func(args)
File "/anaconda3/envs/MITY/lib/python3.7/site-packages/mitylib/commands.py", line 53, in _cmd_call
args.out_folder_path, args.region)
File "/anaconda3/envs/MITY/lib/python3.7/site-packages/mitylib/call.py", line 108, in do_call
vcfnorm(vcf=unnormalised_vcf_path, out_file=output_file_name, p=p, genome=genome)
File "/anaconda3/envs/MITY/lib/python3.7/site-packages/mitylib/normalise.py", line 1313, in do_normalise
single_allele = split_multi_allelic(variants)
File "/anaconda3/envs/MITY/lib/python3.7/site-packages/mitylib/normalise.py", line 233, in split_multi_allelic
AD_idx = FORMAT_name.index("AD")
ValueError: 'AD' is not in list