git clone fails due to broken link

[plavskin]

It looks like the rapidjson github repository has moved (potentially to here), and as a result, git clone --recursive no longer works on this repository.

[ekg]

Thanks for the catch. As a matter of current practice I'm making release tarballs that include the submodules. We can fix this repo, but... This is extremely old software that's full of bugs and has been superceded by vg (vgteam/VG). You'd want to "surject" the output of vg map/mpmap/giraffe to BAM to get the same kind of result as that provided by glia.

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On Mon, Aug 16, 2021, 06:14 Eugene Plavskin ***@***.***> wrote: It looks like the rapidjson github repository has moved (potentially to here <https://github.com/Tencent/rapidjson>), and as a result, git clone --recursive no longer works on this repository. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#3>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDQENH6P4VKP3GPNQYLYTT5CGBZANCNFSM5CG5XH2Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .

[plavskin]

Thank you so much for the suggestion! I was looking to follow part of the analysis pipeline from the 2015 1000G paper (specifically, pooling initial genotype calls from multiple callers and then re-genotyping those sites with FreeBayes), which brought me here.

Is realignment of reads around candidate variable sites still recommended before calling genotypes at those sites with FreeBayes? (The FreeBayes documentation seems to say it's not)