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3. Error remove 0x1 from alternate contigs tutorial

Hi Genevieve Brandt. Unfortunately, after downgrading samtools to v1.3.1, the code using the tutorial ( https://gatk.broadinstitute.org/hc/en-us/articles/360037498992--How-to-Map-reads-to-a-referen...

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• Linda Do
• April 08, 2021 21:35
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3. Error remove 0x1 from alternate contigs tutorial

I am currently using v1.11. Do I need to downgrade to v1.3.1 for this tutorial?

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• Linda Do
• April 06, 2021 01:34
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3. Map reads with alternate contigs

Thank you for your answer! I will try it!

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• Linda Do
• April 05, 2021 05:22
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3. Error HaplotypeCaller from alternate contigs tutorial

Thank you for answering! So should I use the GATK3 version of HaplotypeCaller for this step? Are the HaplotypeCaller from GATK3 and HaplotypeCaller from GATK4 very different? Are there benefits to ...

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• Linda Do
• April 01, 2021 02:32
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3. Alt Contig tutorial question

Thank you for your help!

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• Linda Do
• March 25, 2021 20:54
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3. Alt Contig tutorial question

So for clarification, so altalt.sam is indeed the same as 8017bwamem.sam? And these 2 commands should indeed come before steps 4 through 6.1? Thank you in advance!  

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• Linda Do
• March 25, 2021 20:00
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Thank you for your answer. So for clarification, does this mean that the correct workflow 3 would be: bwa mem chr19chr19KI270866v1alt.fasta 8017read1.fq 8017read2.fq > 8017bwamem.samk8 bwa-postalt....

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• Linda Do
• March 24, 2021 18:13
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