Eulemur flavifrons fastq file for PSMC

This fastq file was generated from the all-sites vcf file for Harlow (the E. flavifrons individual used for the de novo assembly), and was used to infer historic Ne using PSMC (Li and Durbin 2011). The vcf was generated by running GATK (McKenna et al. 2010; DePristo et al. 2011) on the filtered bam file (mapping quality 20 or above, PE reads aligned to the same scaffold with correctly oriented read pairs mapping within three standard deviations of the mean, duplicates removed), with the EMIT_ALL_SITES option and a minimum base quality of 20. The fastq was generated from this all-sites vcf using the vcf2fq function within the vcfutils.pl script, using a minimum depth of 26 and a maximum depth of 104 (0.5 and 2x the mean depth, respectively), and a minimum quality (QUAL*GQ) of 20.