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Old 03-22-2016, 05:51 AM   #1
Mark
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Location: Raleigh, NC

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Default freebayes haplotype calling (phased variants)

Hi All

I often use freebayes for variant calling and am pleased with the results. Now I want to use it to call haplotypes. The nature of my project is that I wish to phase variants in 400-450bp amplicons. These amplicons are generated from a mixed target source such that different targets within it will generate amplicons of slightly different sequence though different targets may share one or more specific variants. My plan was to subject these amplicons to 2X300 bp Illumina sequencing, merge read 1 and read 2, then align to a reference. The freebayes documentation indicates that the “-E” flag is required to call phased variants, and so I’ve included “-E 400” in my command line. I then tested this against simulated reads I made that contain a 2bp and 3bp deletion 11bp apart. While both deletions are called by freebayes I see nothing that indicates they are phased. I had read online that I might expect these two variants to be depicted by freebayes as a single "complex" variant bound by the 2 deletions. I do not. Moreover, in the header I see the following: "##phasing=none". Am I mistaken about how freebayes reports phased variants or is there something more to the proper command line that I am missing?

Thanks

Mark

Example:

freebayes version: v1.0.2-14-g9e98366

Code:
$ freebayes -F 0.1 -E 400 -f target.ref.fa -v outE400F0.10.new  out.ref.sort.bam

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  unknown
target  186     .       TAGAGGCTGCGTACGGGTAACACGTCGTAAGGAGCGATGACGCGGGCACTGCTCCGGCGTCGTCGA	TAGAGGCTGCGTACGGGTAACACGTCGTAAGGAGCGATGACGCGGGCACTGCTCCGGCGTCGTA      2403.38 .       AB=0;ABP=0;AC=2;AF=1;AN=2;AO=280;CIGAR=63M2D1M;DP=993;DPB=962.909;DPRA=0;EPP=4.53033;EPPR=0;GTI=0;LEN=2;MEANALT=452;MQM=17;MQMR=0;NS=1;NUMALT=1;ODDS=388.578;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4320;QR=0;RO=0;RPL=280;RPP=611.023;RPPR=0;RPR=0;RUN=1;SAF=147;SAP=4.53033;SAR=133;SRF=0;SRP=0;SRR=0;TYPE=del     GT:DP:DPR:RO:QR:AO:QA:GL        1/1:993:993,280:0:0:280:4320:-327.573,-84.2884,0
target  261     .       TGAGGTGGAGGCGA  TGAGGTGGAGA     7515.8  .       AB=0;ABP=0;AC=2;AF=1;AN=2;AO=787;CIGAR=1M3D10M;DP=981;DPB=775.071;DPRA=0;EPP=5.02174;EPPR=0;GTI=0;LEN=3;MEANALT=37;MQM=17;MQMR=0;NS=1;NUMALT=1;ODDS=1091.43;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=13337;QR=0;RO=0;RPL=787;RPP=1711.96;RPPR=0;RPR=0;RUN=1;SAF=380;SAP=5.02174;SAR=407;SRF=0;SRP=0;SRR=0;TYPE=del     GT:DP:DPR:RO:QR:AO:QA:GL      1/1:981:981,787:0:0:787:13337:-991.985,-236.911,0

Last edited by GenoMax; 03-22-2016 at 06:06 AM. Reason: added CODE tags to improve readability
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Old 03-23-2016, 04:31 AM   #2
GenoMax
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For reference cross-posted: https://www.biostars.org/p/182974/
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