Good afternoon, I'm trying to do the SNP calling of some files from a target-capture sequencing experiment with GATK. I don't have any problem but I've seen that with Freebayes I can do the SNP calling specifically of my target genes, and this would help me a lot to get the fasta files

freebayes --fasta-reference /ufrc/rgenomics/share/Probe_Design/Podarcis/POR_100801/ANALYSIS/POR_100801_File1_2_3.fasta --bam-list /ufrc/rgenomics/share/Data_Analysis/TARGETseq/POR_1008/POR_100801/6_FreeBayes/6.1/list_of_bams.txt --targets /ufrc/rgenomics/share/Data_Analysis/TARGETseq/POR_1008/POR_100801/6_FreeBayes/6.2/RG_6702_Probes_noOverlap_nomito_split/pt100_RG_6702_Probes_noOverlap_nomito.bed --max-complex-gap 1 --theta 0.01 --ploidy 2 --min-alternate-fraction 0.2 --min-alternate-count 2 --min-coverage 8 --min-mapping-quality 1 --min-base-quality 20 --report-genotype-likelihood-max --no-complex --no-mnps --no-indels

Do you know if I can do this with HaplotypeCaller or GenotypeGVCFs? I would really appreciate your help, as is almost the last step I need to obtain the fasta files. Thank you!!