add prep_known_variant_vcf_pf

according to the [method document](http://ngs.sanger.ac.uk/production/malaria/pfcommunityproject/Pf6/Pf_6_extended_methods.pdf) of [MalariaGen Pfv6 paper](https://wellcomeopenresearch.org/articles/6-42) #3

ref/prep_known_variant_vcf_pf.py

@@ -0,0 +1,49 @@
+from subprocess import run
+import ftplib
+from pathlib import Path
+
+# file names and folders
+Path("orig").mkdir(parents=True, exist_ok=True)
+Path("filt").mkdir(parents=True, exist_ok=True)
+remote_filename_lst = "3d7_hb3.gatk.final.vcf.gz 7g8_gb4.gatk.final.vcf.gz hb3_dd2.gatk.final.vcf.gz".split()
+local_filename_lst = [f"orig/{fn}" for fn in remote_filename_lst]
+filt_filename_lst = [
+    f"filt/{Path(fn).name.replace('final', 'final.pass')}" for fn in remote_filename_lst
+]
+
+
+# DOWNLOAD VCF from pfcrosses1.0
+
+ftp_server = ftplib.FTP("ngs.sanger.ac.uk")
+ftp_server.login()
+ftp_server.cwd("/production/malaria/pf-crosses/1.0/")
+for remote_filename, local_filename in zip(remote_filename_lst, local_filename_lst):
+    with open(local_filename, "wb") as file:
+        print("download " + remote_filename)
+        ftp_server.retrbinary("RETR " + remote_filename, file.write)
+ftp_server.quit()
+
+
+# FILTER and MERGE VCF files
+
+for origf, passf in zip(local_filename_lst, filt_filename_lst):
+    print("filter " + origf)
+    res = run(
+        f"""
+        bcftools view -f PASS {origf} -Oz -o {passf}
+        bcftools index {passf}
+        """,
+        shell=True,
+        capture_output=True,
+        text=True,
+    )
+    assert res.returncode == 0
+
+print("merge filtered vcfs")
+run(
+    "bcftools merge --force-samples {}  -Oz -o known_variants.vcf.gz".format(
+        " ".join(filt_filename_lst)
+    ),
+    shell=True,
+)
+assert res.returncode == 0